A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
See the code
# One-time use (no install required)
npx bioskill install
# Or install globally for repeated use
npm install -g bioskill
bioskill install
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
Now tracking NVIDIA BioNeMo Agent Toolkit, Claude Science built-in skills, and the emerging ecosystem of agent-callable tools for life sciences.
1,722 deduplicated skills from 22 open-source repositories, organized into 16 categories. Each skill is a self-contained SKILL.md folder compatible with Claude-based agent frameworks (OpenClaw, NanoClaw, Biomni).
This project is created and maintained by BioTender.
BioTender is a Chinese AI-for-Biology intelligence and media platform covering protein design, structure prediction, virtual cells, AI drug discovery, biological foundation models, scientific agents, AI4Bio startups, and frontier research.
526 skills — WGS/WES analysis, variant annotation, GWAS, CNV, structural variants, haplotype phasing, genome assembly.
| Skill | Source | Description |
|---|---|---|
| bio-alignment-amplicon-clipping | bioskills | Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer pan... |
| bio-alignment-filtering | bioskills | Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality al... |
| bio-alignment-indexing | bioskills | Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific... |
| bio-alignment-io | bioskills | Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and othe... |
| bio-alignment-msa-parsing | bioskills | Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations,... |
| bio-alignment-msa-statistics | bioskills | Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing... |
| bio-alignment-multiple | bioskills | Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, seq... |
| bio-alignment-pairwise | bioskills | Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scorin... |
| bio-alignment-sorting | bioskills | Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end... |
| bio-alignment-structural | bioskills | Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coor... |
| bio-alignment-trimming | bioskills | Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when re... |
| bio-alignment-validation | bioskills | Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when... |
| bio-atac-seq-allele-specific-accessibility | bioskills | Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic v... |
| bio-atac-seq-atac-peak-calling | bioskills | Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligne... |
| bio-atac-seq-consensus-peakset | bioskills | Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and major... |
| bio-bam-statistics | bioskills | Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating cove... |
| bio-basecalling | bioskills | Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified b... |
| bio-bedgraph-handling | bioskills | Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization,... |
| bio-biomart-queries | bioskills | Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use... |
| bio-causal-genomics-colocalization-analysis | bioskills | Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR,... |
| bio-causal-genomics-effector-gene-prioritization | bioskills | Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021),... |
| bio-causal-genomics-fine-mapping | bioskills | Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, M... |
| bio-causal-genomics-genetic-correlation | bioskills | Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL,... |
| bio-causal-genomics-genomic-sem | bioskills | Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor... |
| bio-causal-genomics-mediation-analysis | bioskills | Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-st... |
| bio-causal-genomics-mendelian-randomization | bioskills | Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egge... |
| bio-causal-genomics-pleiotropy-detection | bioskills | Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiot... |
| bio-causal-genomics-proteome-mr-drug-target | bioskills | Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP... |
| bio-causal-genomics-transcriptome-wide-association | bioskills | Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-Mu... |
| bio-cfdna-preprocessing | bioskills | Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal usi... |
| bio-chipseq-allele-specific-binding | bioskills | Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter;... |
| bio-chipseq-chip-deep-learning | bioskills | Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft moti... |
| bio-chipseq-peak-calling | bioskills | Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size m... |
| bio-chipseq-visualization | bioskills | Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven trac... |
| bio-clinical-biostatistics-adaptive-designs | bioskills | Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Frie... |
| bio-clinical-biostatistics-categorical-tests | bioskills | Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern M... |
| bio-clinical-biostatistics-power-sample-size | bioskills | Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equ... |
| bio-clinical-databases-acmg-classification | bioskills | Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pe... |
| bio-clinical-databases-clinvar-lookup | bioskills | Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF... |
| bio-clinical-databases-dbsnp-queries | bioskills | Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build... |
...and 486 additional genomics skills in the skills/bioskills/, skills/openclaw/, skills/sciagent/ directories.
167 skills — mass spectrometry analysis, structure prediction, protein design, binding affinity optimization.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-nucleosome-positioning | bioskills | Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter.... |
| bio-data-visualization-sequence-logos | bioskills | Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability... |
| bio-generative-design | bioskills | Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based ge... |
| bio-hi-c-analysis-hic-differential | bioskills | Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significan... |
| bio-hi-c-analysis-tad-detection | bioskills | Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and... |
| bio-immunoinformatics-mhc-binding-prediction | bioskills | Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from pr... |
| bio-immunoinformatics-neoantigen-prediction | bioskills | Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient... |
| bio-interaction-databases | bioskills | Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use... |
| bio-ml-docking-rescoring | bioskills | Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity)... |
| bio-molecular-io | bioskills | Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handl... |
| bio-molecular-standardization | bioskills | Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping,... |
| bio-pdb-geometric-analysis | bioskills | Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing st... |
| bio-pdb-structure-io | bioskills | Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB,... |
| bio-pdb-structure-modification | bioskills | Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-... |
| bio-pdb-structure-navigation | bioskills | Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over st... |
| bio-phylo-tree-manipulation | bioskills | Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collap... |
| bio-population-genetics-population-structure | bioskills | Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions,... |
| bio-pose-validation | bioskills | Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planar... |
| bio-primer-design-primer-validation | bioskills | Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complement... |
| bio-protac-degraders | bioskills | Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (l... |
| bio-proteomics-data-import | bioskills | Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Use when star... |
| bio-proteomics-dia-analysis | bioskills | Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free... |
| bio-proteomics-peptide-identification | bioskills | Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searc... |
| bio-proteomics-protein-inference | bioskills | Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles protein groups and... |
| bio-proteomics-quantification | bioskills | Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic label... |
| bio-proteomics-spectral-libraries | bioskills | Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-base... |
| bio-qsar-modeling | bioskills | Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handl... |
| bio-rna-structure-ncrna-search | bioskills | Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database. Identifies str... |
| bio-rna-structure-structure-probing | bioskills | Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucle... |
| bio-scaffold-analysis | bioskills | Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis v... |
| bio-similarity-searching | bioskills | Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules... |
| bio-structural-biology-alphafold-predictions | bioskills | Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures,... |
| bio-structural-biology-modern-structure-prediction | bioskills | Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel prot... |
| bio-substructure-search | bioskills | Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticit... |
| bio-transcription-translation | bioskills | Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using... |
| bio-virtual-screening | bioskills | Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice ru... |
| adhd-daily-planner | openclaw | Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-a... |
| alphafold-database | openclaw | Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (... |
| antibody-design-agent | openclaw | An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion). |
| bindingdb-database | openclaw | Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathoge... |
...and 127 additional proteomics skills in the skills/kdense/, skills/openclaw/, skills/sciagent/ directories.
144 skills — preprocessing, clustering, cell type annotation, trajectory inference, cell communication, multimodal integration.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-co-accessibility | bioskills | Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linki... |
| bio-atac-seq-deep-learning-atac | bioskills | Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond... |
| bio-atac-seq-enhancer-gene-linking | bioskills | Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target g... |
| bio-atac-seq-motif-deviation | bioskills | Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correl... |
| bio-atac-seq-single-cell-atac | bioskills | Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (pai... |
| bio-causal-genomics-heritability-partitioning | bioskills | Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level gen... |
| bio-chipseq-chromatin-state-segmentation | bioskills | Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate H... |
| bio-chipseq-peak-annotation | bioskills | Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPsee... |
| bio-clip-seq-stamp-antibody-free | bioskills | Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), T... |
| bio-crispr-screens-combinatorial-screens | bioskills | Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021)... |
| bio-crispr-screens-perturb-seq-analysis | bioskills | Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a s... |
| bio-data-visualization-dimensionality-reduction-plots | bioskills | Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, loc... |
| bio-data-visualization-matplotlib-fundamentals | bioskills | Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (... |
| bio-expression-matrix-normalization | bioskills | Normalize and transform RNA-seq count matrices for differential expression, visualization, and clustering. Covers between-sample (TMM, RLE, upper q... |
| bio-expression-matrix-sparse-handling | bioskills | Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where m... |
| bio-flow-cytometry-clustering-phenotyping | bioskills | Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discover... |
| bio-flow-cytometry-doublet-detection | bioskills | Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering... |
| bio-flow-cytometry-doublet-detection | bioskills | Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering... |
| bio-gene-regulatory-networks-coexpression-networks | bioskills | Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detect... |
| bio-gene-regulatory-networks-multiomics-grn | bioskills | Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data using SCENIC+ to identify eRegulons linking tra... |
| bio-gene-regulatory-networks-scenic-regulons | bioskills | Infer gene regulatory networks and identify transcription factor regulons from single-cell RNA-seq data using pySCENIC. Discovers co-expression mod... |
| bio-imaging-mass-cytometry-cell-segmentation | bioskills | Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segme... |
| bio-imaging-mass-cytometry-interactive-annotation | bioskills | Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation val... |
| bio-imaging-mass-cytometry-phenotyping | bioskills | Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assign... |
| bio-imaging-mass-cytometry-spatial-analysis | bioskills | Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when... |
| bio-machine-learning-atlas-mapping | bioskills | Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without r... |
| bio-methylation-dmr-detection | bioskills | Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions... |
| bio-read-qc-umi-processing | bioskills | Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate... |
| bio-single-cell-batch-integration | bioskills | Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biologic... |
| bio-single-cell-cell-annotation | bioskills | Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell l... |
| bio-single-cell-cell-communication | bioskills | Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use when i... |
| bio-single-cell-clustering | bioskills | Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clu... |
| bio-single-cell-data-io | bioskills | Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad... |
| bio-single-cell-doublet-detection | bioskills | Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and s... |
| bio-single-cell-doublet-detection | bioskills | Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and s... |
| bio-single-cell-lineage-tracing | bioskills | Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or d... |
| bio-single-cell-markers-annotation | bioskills | Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for differential expression between clus... |
| bio-single-cell-metabolite-communication | bioskills | Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. Predict metabolite secreti... |
| bio-single-cell-multimodal-integration | bioskills | Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA... |
| bio-single-cell-perturb-seq | bioskills | Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturb... |
...and 104 additional single-cell analysis skills in the skills/openclaw/, skills/bioskills/, skills/sciagent/ directories.
236 skills — medical AI, clinical decision support, drug discovery, general biological tools.
| Skill | Source | Description |
|---|---|---|
| bio-flow-cytometry-bead-normalization | bioskills | Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalizatio... |
| bio-flow-cytometry-fcs-handling | bioskills | Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading an... |
| bio-immunoinformatics-tcr-epitope-binding | bioskills | Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to their cognate epitope... |
| bio-molecular-descriptors | bioskills | Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descript... |
| bio-phylo-divergence-dating | bioskills | Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenie... |
| bio-phylo-species-trees | bioskills | Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows ge... |
| bio-phylo-tree-io | bioskills | Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, conver... |
| bio-reporting-quarto-reports | bioskills | Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS. Use when creating... |
| bio-ribo-seq-ribosome-stalling | bioskills | Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause si... |
| aav-vector-design-agent | openclaw | AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization. |
| ai-analyzer | openclaw | AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。 |
| bayesian-optimizer | openclaw | Bayesian Optimize |
| biokernel | openclaw | Biomedical OS Core & MCP Server |
| biologist-analyst | openclaw | Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology framework... |
| biomcp-server | openclaw | MCP bio bridge |
| brainstorming | openclaw | You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user int... |
| cellagent-annotation | openclaw | Cell tagger |
| chemist-analyst | openclaw | Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectro... |
| computational-pathology-agent | openclaw | Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction. |
| crisis-response-protocol | openclaw | Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or su... |
| crispr-guide-design | openclaw | Guide foundry |
| data-transform | openclaw | Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.). |
| differentiation-schemes | openclaw | Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes, buildin... |
| dispatching-parallel-agents | openclaw | Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies |
| emergency-card | openclaw | 生成紧急情况下快速访问的医疗信息摘要卡片。当用户需要旅行、就诊准备、紧急情况或询问"紧急信息"、"医疗卡片"、"急救信息"时使用此技能。提取关键信息（过敏、用药、急症、植入物），支持多格式输出（JSON、文本、二维码），用于急救或快速就医。 |
| epidemiologist-analyst | openclaw | Analyzes disease patterns and health events through epidemiological lens using surveillance systems, outbreak investigation methods, and disease mo... |
| executing-plans | openclaw | Use when you have a written implementation plan to execute in a separate session with review checkpoints |
| family-health-analyzer | openclaw | 分析家族病史、评估遗传风险、识别家庭健康模式、提供个性化预防建议 |
| fhir-developer-skill | openclaw | FHIR API development guide for building healthcare endpoints. Use when: (1) Creating FHIR REST endpoints (Patient, Observation, Encounter, Conditio... |
| find-skills | openclaw | Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", o... |
| fitness-analyzer | openclaw | 分析运动数据、识别运动模式、评估健身进展，并提供个性化训练建议。支持与慢性病数据的关联分析。 |
| goal-analyzer | openclaw | 分析健康目标数据、识别目标模式、评估目标进度,并提供个性化目标管理建议。支持与营养、运动、睡眠等健康数据的关联分析。 |
| grief-companion | openclaw | Compassionate bereavement support, memorial creation, grief education, and healing journey guidance. Specializes in understanding grief stages, cre... |
| health-trend-analyzer | openclaw | 分析一段时间内健康数据的趋势和模式。关联药物、症状、生命体征、化验结果和其他健康指标的变化。识别令人担忧的趋势、改善情况，并提供数据驱动的洞察。当用户询问健康趋势、模式、随时间的变化或"我的健康状况有什么变化？"时使用。支持多维度分析（体重/BMI、症状、药物依从性、化验结果、情绪睡眠），相关... |
| hipaa-compliance | openclaw | Ensure HIPAA compliance when handling PHI (Protected Health Information). Use when writing code that accesses user health data, check-ins, journal... |
| kragen-knowledge-graph | openclaw | Graph-RAG Solver |
| leads-literature-mining | openclaw | Review Automator |
| medical-imaging-review | openclaw | Write comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses... |
| mental-health-analyzer | openclaw | 分析心理健康数据、识别心理模式、评估心理健康状况、提供个性化心理健康建议。支持与睡眠、运动、营养等其他健康数据的关联分析。 |
| mesh-generation | openclaw | Plan and evaluate mesh generation for numerical simulations. Use when choosing grid resolution, checking aspect ratios/skewness, estimating mesh qu... |
...and 196 additional biology and ai skills in the skills/nobel/, skills/openclaw/, skills/neuroclaw/ directories.
152 skills — EHR analysis, clinical trial design, drug interactions, precision medicine, adverse event detection.
| Skill | Source | Description |
|---|---|---|
| bio-admet-prediction | bioskills | Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handlin... |
| bio-clinical-biostatistics-bayesian-trials | bioskills | Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtur... |
| bio-clinical-biostatistics-cdisc-data | bioskills | Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM archit... |
| bio-clinical-biostatistics-effect-measures | bioskills | Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen,... |
| bio-clinical-biostatistics-logistic-regression | bioskills | Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 202... |
| bio-clinical-biostatistics-missing-data | bioskills | Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-b... |
| bio-clinical-biostatistics-multiplicity-graphical | bioskills | Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, m... |
| bio-clinical-biostatistics-subgroup-analysis | bioskills | Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction t... |
| bio-clinical-biostatistics-trial-reporting | bioskills | Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guida... |
| bio-clinical-databases-polygenic-risk | bioskills | Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS... |
| bio-covalent-design | bioskills | Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartat... |
| bio-systems-biology-gene-essentiality | bioskills | Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and ide... |
| bio-workflows-clinical-trial-pipeline | bioskills | End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regula... |
| bio-workflows-outbreak-pipeline | bioskills | End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating,... |
| agentd-drug-discovery | openclaw | Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks. |
| autonomous-oncology-agent | openclaw | Precision Oncology |
| biomedical-search | openclaw | Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search. |
| cancer-metabolism-agent | openclaw | AI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilitie... |
| cart-design-optimizer-agent | openclaw | AI-guided CAR-T cell design for solid tumors using antigen prioritization, safety-by-design architectures, and exhaustion-resistant engineering. |
| cellular-senescence-agent | openclaw | AI-powered analysis of cellular senescence for aging research, cancer therapy response, and senolytic drug development. |
| chatehr-clinician-assistant | openclaw | EHR Chat Assistant |
| chematagent-drug-discovery | openclaw | Chemical Lab Agent |
| chemcrow-drug-discovery | openclaw | An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design. |
| chemical-property-lookup | openclaw | Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools. |
| chromosomal-instability-agent | openclaw | AI-powered analysis of chromosomal instability (CIN) signatures for cancer prognosis, immunotherapy response prediction, and therapeutic vulnerabil... |
| clinical-diagnostic-reasoning | openclaw | Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application. For dia... |
| clinical-trial-protocol-skill | openclaw | Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Gener... |
| clinical-trials-search | openclaw | Search ClinicalTrials.gov with natural language queries. Find clinical trials, enrollment, and outcomes using Valyu semantic search. |
| clinicaltrials-database | openclaw | Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, f... |
| ctdna-dynamics-mrd-agent | openclaw | AI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse predi... |
| cytokine-storm-analysis-agent | openclaw | AI-powered cytokine release syndrome (CRS) and cytokine storm analysis for prediction, monitoring, and management in immunotherapy and infectious d... |
| datacommons-client | openclaw | Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with d... |
| drug-discovery-search | openclaw | End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu. |
| drug-interaction-checker | openclaw | Checks for potential drug-drug interactions (DDIs) between a list of medications. |
| drug-labels-search | openclaw | Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu. |
| drugbank-search | openclaw | Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu. |
| exosome-ev-analysis-agent | openclaw | AI-powered extracellular vesicle and exosome analysis for cancer biomarker discovery, liquid biopsy applications, and intercellular communication p... |
| immune-checkpoint-combination-agent | openclaw | AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular prof... |
| liquid-biopsy-analytics-agent | openclaw | Comprehensive analysis of liquid biopsy data (ctDNA, CTCs) for cancer detection, MRD monitoring, and response tracking. |
| medical-entity-extractor | openclaw | Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages. |
...and 112 additional clinical and medical skills in the skills/drugclaw/, skills/openclaw/, skills/sciagent/ directories.
97 skills — RNA-seq full pipeline, differential expression, alternative splicing, lncRNA, small RNA.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-differential-accessibility | bioskills | Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessib... |
| bio-chipseq-differential-binding | bioskills | Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices... |
| bio-chipseq-spike-in-normalization | bioskills | Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CU... |
| bio-clip-seq-ago-clip-mirna-targets | bioskills | Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (... |
| bio-clip-seq-binding-site-annotation | bioskills | Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with... |
| bio-clip-seq-differential-clip | bioskills | Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sli... |
| bio-codon-usage | bioskills | Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences... |
| bio-crispr-screens-batch-correction | bioskills | Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative... |
| bio-crispr-screens-batch-correction | bioskills | Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative... |
| bio-data-visualization-network-visualization | bioskills | Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamad... |
| bio-data-visualization-volcano-and-ma-plots | bioskills | Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement... |
| bio-de-deseq2-basics | bioskills | Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, runni... |
| bio-de-edger-basics | bioskills | Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test frame... |
| bio-de-results | bioskills | Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multipl... |
| bio-differential-expression-batch-correction | bioskills | Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting... |
| bio-differential-expression-batch-correction | bioskills | Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting... |
| bio-differential-expression-timeseries-de | bioskills | Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when... |
| bio-differential-splicing | bioskills | Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial... |
| bio-epitranscriptomics-m6a-differential | bioskills | Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or c... |
| bio-epitranscriptomics-m6a-peak-calling | bioskills | Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data. |
| bio-epitranscriptomics-m6anet-analysis | bioskills | Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read... |
| bio-expression-matrix-counts-ingest | bioskills | Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantific... |
| bio-flow-cytometry-differential-analysis | bioskills | Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testi... |
| bio-gene-regulatory-networks-differential-networks | bioskills | Compare gene regulatory and co-expression networks between biological conditions to identify rewired regulatory relationships using DiffCorr. Detec... |
| bio-gene-regulatory-networks-perturbation-simulation | bioskills | Simulate transcription factor perturbation effects on cell state using CellOracle, which integrates GRN inference with in silico knockout and overe... |
| bio-geo-data | bioskills | Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, nav... |
| bio-immunoinformatics-immunogenicity-scoring | bioskills | Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and seque... |
| bio-isoform-switching | bioskills | Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protei... |
| bio-metabolomics-statistical-analysis | bioskills | Statistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes... |
| bio-methylation-differential-cpg | bioskills | Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage... |
| bio-microbiome-differential-abundance | bioskills | Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying t... |
| bio-microbiome-differential-abundance | bioskills | Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying t... |
| bio-multi-omics-mofa-integration | bioskills | Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variat... |
| bio-pathway-go-enrichment | bioskills | Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from d... |
| bio-pathway-gsea | bioskills | Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes i... |
| bio-proteomics-differential-abundance | bioskills | Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and D... |
| bio-proteomics-differential-abundance | bioskills | Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and D... |
| bio-reverse-complement | bioskills | Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or conver... |
| bio-ribo-seq-translation-efficiency | bioskills | Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between con... |
| bio-rna-quantification-tximport-workflow | bioskills | Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when i... |
...and 57 additional transcriptomics skills in the skills/bioskills/, skills/openclaw/, skills/omicsclaw/ directories.
63 skills — UniProt, PDB, KEGG, Reactome, GEO, ClinVar, Ensembl, STRING.
| Skill | Source | Description |
|---|---|---|
| bio-batch-downloads | bioskills | Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of... |
| bio-data-visualization-ggplot2-fundamentals | bioskills | Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with... |
| bio-motif-search | bioskills | Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulat... |
| bio-restriction-sites | bioskills | Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially... |
| bio-retrosynthesis | bioskills | Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynF... |
| biomni-general-agent | openclaw | Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions. |
| biomni-research-agent | openclaw | Bio-Research Generalist |
| chembl-search | openclaw | Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search. |
| deep-research | openclaw | Execute autonomous multi-step deep research on any topic. Use when the user asks for comprehensive research, literature reviews, competitive analys... |
| deep-research-swarm | openclaw | Multi-agent research literature analysis |
| knowledge-synthesis | openclaw | Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on fres... |
| labstep | openclaw | Interact with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities. |
| literature-search | openclaw | Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search. |
| mcpmed-bioinformatics-server | openclaw | Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser. |
| medrxiv-search | openclaw | Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search. |
| nonlinear-solvers | openclaw | Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration,... |
| patents-search | openclaw | Search global patents with natural language queries. Prior art, patent landscapes, and innovation tracking via Valyu. |
| perplexity-search | openclaw | Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when condu... |
| pubmed-search | openclaw | Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks abo... |
| research-grants | openclaw | Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts... |
| research-literature | openclaw | Research Literature agent for healthcare workflows. |
| research-lookup | openclaw | Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects th... |
| scientific-problem-selection | openclaw | This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic... |
| search-strategy | openclaw | Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries... |
| virtual-lab-agent | openclaw | AI-powered virtual laboratory orchestrating multi-agent scientific research teams for autonomous hypothesis generation, experimental design, and va... |
| biorxiv-database | sciagent | Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, v... |
| geopandas-geospatial | sciagent | Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric... |
| plotly-interactive-visualization | sciagent | Interactive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan. Two APIs: Plotly Express (Da... |
| pymoo | sciagent | Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve wit... |
| scikit-learn-machine-learning | sciagent | Classical ML in Python: classification, regression, clustering, dim reduction, evaluation, tuning, preprocessing pipelines. Linear models, tree ens... |
| scikit-survival-analysis | sciagent | Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-... |
| uspto-database | sciagent | Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; downlo... |
| eqtl-catalogue-region-fetch | clawbio | Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for ev... |
| ncbi-datasets | clawbio | Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools. |
| turingdb-graph | clawbio | Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning. |
| ukb-navigator | clawbio | Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your |
| bio-dataset-search | bioclaw | Step 3: Dataset search and task matching (数据集搜索与匹配) |
| bio-tools | bioclaw | Biology research tools reference. Always available inside agent containers. |
| aeon | kdense | This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection,... |
| citation-management | kdense | Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations... |
...and 23 additional database query skills in the skills/kdense/, skills/labclaw/, skills/omics/ directories.
69 skills — MOFA, DIABLO, single-cell multimodal, spatial transcriptomics.
| Skill | Source | Description |
|---|---|---|
| bio-clinical-biostatistics-survival-analysis | bioskills | Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival tim... |
| bio-clinical-biostatistics-survival-analysis | bioskills | Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival tim... |
| bio-machine-learning-biomarker-discovery | bioskills | Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use wh... |
| bio-machine-learning-model-validation | bioskills | Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets. Prevents data leakage and overfittin... |
| bio-machine-learning-prediction-explanation | bioskills | Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive cl... |
| bio-machine-learning-survival-analysis | bioskills | Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival mode... |
| bio-machine-learning-survival-analysis | bioskills | Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival mode... |
| bio-metabolomics-lipidomics | bioskills | Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-... |
| bio-metabolomics-metabolite-annotation | bioskills | Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when... |
| bio-metabolomics-normalization-qc | bioskills | Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use whe... |
| bio-metabolomics-targeted-analysis | bioskills | Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use w... |
| bio-multi-omics-mixomics-analysis | bioskills | Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant a... |
| bio-multi-omics-similarity-network | bioskills | Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity... |
| bio-data-visualization-specialized-omics-plots | openclaw | Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, bo... |
| biomedical-data-analysis | openclaw | Omics data forge |
| dask | openclaw | Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clu... |
| digital-twin-clinical-agent | openclaw | AI-powered patient digital twin creation for clinical trial simulation, treatment outcome prediction, and personalized medicine using real-world da... |
| ehr-fhir-integration | openclaw | Provides comprehensive tools for working with Electronic Health Records (EHR) using the HL7 FHIR standard. |
| infographics | openclaw | Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates researc... |
| labarchive-integration | openclaw | Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap... |
| latex-posters | openclaw | Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters,... |
| medea-therapeutic-discovery | openclaw | An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literat... |
| multi-search-engine | openclaw | Multi search engine integration with 17 engines (8 CN + 9 Global). Supports advanced search operators, time filters, site search, privacy engines,... |
| numerical-integration | openclaw | Select and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances, adapt... |
| opentrons-integration | openclaw | Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), lab... |
| pptx-posters | openclaw | Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX p... |
| pyzotero | openclaw | Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags... |
| seaborn | openclaw | Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attr... |
| tooluniverse-immunotherapy-response-prediction | openclaw | Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and opti... |
| tooluniverse-metabolomics | openclaw | Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (22... |
| wellally-tech | openclaw | Integrate digital health data sources (Apple Health, Fitbit, Oura Ring) and connect to WellAlly.tech knowledge base. Import external health device... |
| zarr-python | openclaw | Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific... |
| brenda-database | sciagent | BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism dat... |
| kegg-pathway-analysis | sciagent | Guide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling... |
| latex-research-posters | sciagent | Research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure integration, accessibility, and QA... |
| libsbml-network-modeling | sciagent | Build, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1–3, reactions/kinetic laws, species, rules, F... |
| protocolsio-integration | sciagent | protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materia... |
| reactome-database | sciagent | Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis s... |
| database-access | bioclaw_hub | Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources. |
| machine-learning-for-omics | bioclaw_hub | Workflow for predictive modeling, biomarker discovery, survival modeling, and explainability over omics-derived features. |
...and 29 additional multi-omics integration skills in the skills/neuroclaw/, skills/kdense/, skills/bioclaw_hub/ directories.
86 skills — sequence analysis, BLAST, tool chains, pipeline management.
| Skill | Source | Description |
|---|---|---|
| bio-batch-processing | bioskills | Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operati... |
| bio-compressed-files | bioskills | Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexa... |
| bio-filter-sequences | bioskills | Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted record... |
| bio-flow-cytometry-compensation-transformation | bioskills | Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh t... |
| bio-flow-cytometry-gating-analysis | bioskills | Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifyi... |
| bio-fragment-analysis | bioskills | Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fra... |
| bio-fragment-analysis | bioskills | Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fra... |
| bio-hi-c-analysis-hic-data-io | bioskills | Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and... |
| bio-hi-c-analysis-matrix-operations | bioskills | Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and... |
| bio-imaging-mass-cytometry-data-preprocessing | bioskills | Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when star... |
| bio-imaging-mass-cytometry-quality-metrics | bioskills | Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality... |
| bio-primer-design-primer-basics | bioskills | Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Return... |
| bio-read-qc-quality-filtering | bioskills | Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from rea... |
| bio-restriction-enzyme-selection | bioskills | Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are comm... |
| bio-restriction-fragment-analysis | bioskills | Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis... |
| bio-restriction-fragment-analysis | bioskills | Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis... |
| bio-ribo-seq-orf-detection | bioskills | Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated... |
| bio-ribo-seq-ribosome-periodicity | bioskills | Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determini... |
| bio-seq-objects | bioskills | Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-... |
| bio-sequence-properties | bioskills | Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence compos... |
| bio-sequence-slicing | bioskills | Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence... |
| bio-sequence-statistics | bioskills | Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, genera... |
| bone-marrow-ai-agent | openclaw | AI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images. |
| chemistry-agent | openclaw | Autonomous chemical synthesis & analysis |
| coagulation-thrombosis-agent | openclaw | AI-powered analysis of coagulation disorders, thrombosis risk prediction, anticoagulation management, and platelet function assessment using machin... |
| convergence-study | openclaw | Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification |
| crisis-detection-intervention-ai | openclaw | Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols. Implements suicide ideation det... |
| data-stats-analysis | openclaw | Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY L... |
| hrv-alexithymia-expert | openclaw | Heart rate variability biometrics and emotional awareness training. Expert in HRV analysis, interoception training, biofeedback, and emotional inte... |
| jungian-psychologist | openclaw | Expert in Jungian analytical psychology, depth psychology, shadow work, archetypal analysis, dream interpretation, active imagination, addiction/re... |
| numerical-stability | openclaw | Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diag... |
| openclaw | Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Cla... | |
| performance-profiling | openclaw | Identify computational bottlenecks, analyze scaling behavior, estimate memory requirements, and receive optimization recommendations for any comput... |
| polars | openclaw | Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel... |
| scikit-survival | openclaw | Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored s... |
| statsmodels | openclaw | Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference an... |
| tooluniverse-image-analysis | openclaw | Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification,... |
| umap-learn | openclaw | UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric... |
| using-superpowers | openclaw | Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifyi... |
| usmle | openclaw | Prepare for US medical licensing exams with progress tracking, weak area analysis, question bank management, and residency match planning. |
...and 46 additional bioinformatics utilities skills in the skills/neuroclaw/, skills/sciagent/, skills/kdense/ directories.
48 skills — volcano plots, heatmaps, PCA/UMAP, interactive charts.
| Skill | Source | Description |
|---|---|---|
| bio-copy-number-copy-ratio-segmentation | bioskills | Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov... |
| bio-data-visualization-color-palettes | bioskills | Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monoton... |
| bio-data-visualization-forest-funnel-plots | bioskills | Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot... |
| bio-data-visualization-interactive-visualization | bioskills | Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animation, with awareness of curr... |
| bio-data-visualization-multipanel-figures | bioskills | Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/le... |
| bio-data-visualization-statistical-annotation | bioskills | Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with co... |
| bio-phylo-tree-visualization | bioskills | Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing c... |
| bio-primer-design-qpcr-primers | bioskills | Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints... |
| bio-reporting-figure-export | bioskills | Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submiss... |
| bio-reporting-rmarkdown-reports | bioskills | Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use w... |
| bio-tcr-bcr-analysis-repertoire-visualization | bioskills | Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Us... |
| bio-workflows-hic-pipeline | bioskills | End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualizatio... |
| data-visualization-expert | openclaw | Generate insightful, publication-quality visualizations from complex datasets. |
| data-viz-plots | openclaw | Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.). |
| linear-solvers | openclaw | Select and configure linear solvers for systems Ax=b in dense and sparse problems. Use when choosing direct vs iterative methods, diagnosing conver... |
| markdown-mermaid-writing | openclaw | Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishe... |
| plotly | openclaw | Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, an... |
| post-processing | openclaw | Extract, analyze, and visualize simulation output data. Use for field extraction, time series analysis, line profiles, statistical summaries, deriv... |
| pytorch-lightning | openclaw | Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipe... |
| speech-pathology-ai | openclaw | Expert speech-language pathologist specializing in AI-powered speech therapy, phoneme analysis, articulation visualization, voice disorders, fluenc... |
| vaex | openclaw | Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFra... |
| cell-figure-guide | sciagent | Cell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts, uppercase panel labels, strict... |
| general-figure-guide | sciagent | Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal... |
| matplotlib-scientific-plotting | sciagent | Low-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control o... |
| napari-image-viewer | sciagent | Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis,... |
| networkx-graph-analysis | sciagent | Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, community detection, generator... |
| pyimagej-fiji-bridge | sciagent | Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Au... |
| scikit-image-processing | sciagent | Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed,... |
| statistical-significance-annotation | sciagent | Guide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *, **, ***, ****), matplotlib... |
| reporting-and-figure-export | bioclaw_hub | Workflow for packaging analysis outputs into reproducible reports, clean tables, and publication-ready figure exports. |
| bio-figure-design | bioclaw | Step 6: Figure design (Figure 详细设计) |
| report-template | bioclaw | Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables... |
| neuropixels-analysis | kdense | Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen... |
| scientific-visualization | kdense | Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, err... |
| shap | kdense | Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predict... |
| generate_cell_analysis_charts | labclaw | Domain-specialized chart generator for cell biology video analysis outputs. Consumes structured JSON from analyze_lab_video_cell_behavior or compat... |
| generate_double_column_pdf_report | labclaw | Assembles experimental data, figures, methods, and results into a journal-style double-column PDF report. Uses reportlab or PyMuPDF for programmati... |
| hand-tracking-toolkit | labclaw | Facebook Research Hand Tracking Challenge Toolkit - evaluation and visualization tools for 3D hand tracking. Supports loading HOT3D data, computing... |
| hands-3d-pose | labclaw | High-quality 3D hand pose estimation for egocentric videos from ECCV 2024 (ap229997/hands). Provides 3D joint keypoints and skeleton visualization... |
| hot3d | labclaw | HOT3D (Hand-Object 3D Dataset) by Meta Facebook - multi-view egocentric hand and object 3D tracking for Aria/Quest smart glasses. State-of-the-art... |
...and 8 additional visualization skills in the skills/omics/, skills/labclaw/, skills/medgeclaw/ directories.
38 skills — Snakemake, Nextflow, CWL, WDL.
| Skill | Source | Description |
|---|---|---|
| bio-reporting-jupyter-reports | bioskills | Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when generating automated analysis re... |
| bio-workflow-management-cwl-workflows | bioskills | Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portab... |
| bio-workflow-management-nextflow-pipelines | bioskills | Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building p... |
| bio-workflow-management-snakemake-workflows | bioskills | Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-ba... |
| bio-workflow-management-wdl-workflows | bioskills | Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GAT... |
| bio-workflows-crispr-editing-pipeline | bioskills | End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and special... |
| bio-workflows-cytometry-pipeline | bioskills | End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and stati... |
| bio-workflows-imc-pipeline | bioskills | End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyp... |
| biomaster-workflows | openclaw | Pipeline maestro |
| care-coordination | openclaw | Care Coordination agent for healthcare workflows. |
| claims-appeals | openclaw | Claims Appeals agent for healthcare workflows. |
| fhir-development | openclaw | FHIR Development agent for healthcare workflows. |
| instrument-data-to-allotrope | openclaw | Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill w... |
| lab-results | openclaw | Lab Results agent for healthcare workflows. |
| pdf-processing-pro | openclaw | Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in productio... |
| pylabrobot | openclaw | Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipm... |
| regulatory-drafting | openclaw | Regulatory Drafting agent for healthcare workflows. |
| scikit-learn | openclaw | Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (cluste... |
| simulation-orchestrator | openclaw | Orchestrate multi-simulation campaigns including parameter sweeps, batch jobs, and result aggregation. Use for running parameter studies, managing... |
| single-trajectory-analysis | openclaw | Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks. |
| histolab-wsi-processing | sciagent | WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep... |
| nextflow-workflow-engine | sciagent | Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLU... |
| pylabrobot | sciagent | Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without v... |
| spikeinterface-electrophysiology | sciagent | Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxwell, Blackrock), preprocess, r... |
| sequence-and-format-io | bioclaw_hub | Workflow for foundational sequence parsing, conversion, compression handling, and interval-aware file validation. |
| bioconductor-bridge | clawbio | Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded |
| bio-manuscript-pipeline | bioclaw | End-to-end pipeline from structured research input to a full manuscript plan (一条龙 Pipeline) |
| skills-hub | bioclaw | Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks ab... |
| polars | kdense | Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel... |
| pydicom | kdense | Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying me... |
| scikit-survival | kdense | Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored s... |
| experiment-pipeline | evoskills | Guides structured 4-stage experiment execution with attempt budgets and gate conditions: Stage 1 initial implementation (reproduce baseline), Stage... |
| biomed-dispatch | medgeclaw | Dispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bi... |
| git-workflows | neuroclaw | Advanced git operations beyond add/commit/push. Use when rebasing, bisecting bugs, using worktrees for parallel development, recovering with reflog... |
| hcppipeline-tool | neuroclaw | Use this skill whenever the user wants to perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion)... |
| bio-workflow-methods-docwriter | omics | Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, Q... |
| Gene Panel Selection Workflow | pantheon | End-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be STRICTLY followed: dataset understanding + s... |
| nf-core Pipelines Skills Index | pantheon | Skills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines. |
19 skills — ChIP-seq, ATAC-seq, DNA methylation, Hi-C, chromatin state.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-atac-qc | bioskills | ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, an... |
| bio-atac-seq-footprinting | bioskills | Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites w... |
| bio-chipseq-cut-and-run-tag | bioskills | Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375... |
| bio-chipseq-motif-analysis | bioskills | Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo,... |
| bio-chipseq-qc | bioskills | Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC... |
| bio-chipseq-super-enhancers | bioskills | Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Han... |
| bio-clip-seq-clip-motif-analysis | bioskills | Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-register... |
| bio-clip-seq-clip-qc | bioskills | Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate rep... |
| bio-copy-number-recurrent-cnv | bioskills | Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-leve... |
| bio-hi-c-analysis-compartment-analysis | bioskills | Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments f... |
| bio-hi-c-analysis-loop-calling | bioskills | Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops a... |
| bio-long-read-sequencing-nanopore-methylation | bioskills | Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from n... |
| bio-methylation-based-detection | bioskills | Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific me... |
| pptx | openclaw | Presentation creation, editing, and analysis. When Claude needs to work with presentations (.pptx files) for: (1) Creating new presentations, (2) M... |
| methylation-clock | clawbio | Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files. |
| methylation-cycle | clawbio | Methylation cycle analysis skill for ClawBio. Produces enzymatic activity |
| atac-seq | bioclaw | ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up. |
| chip-seq | bioclaw | ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review. |
| open-notebook | kdense | Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials int... |
15 skills — KEGG, Reactome, GO, GSEA.
| Skill | Source | Description |
|---|---|---|
| bio-pathway-enrichment-visualization | bioskills | Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers... |
| bio-pathway-kegg-pathways | bioskills | KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways... |
| bio-pathway-reactome | bioskills | Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Perf... |
| bio-pathway-wikipathways | bioskills | WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Perf... |
| gsea-enrichment-analysis | openclaw | Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVe... |
| ontology-explorer | openclaw | Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, underst... |
| ontology-mapper | openclaw | Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registered in on... |
| ontology-validator | openclaw | Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, verifying... |
| tooluniverse-gene-enrichment | openclaw | Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supp... |
| query-kegg | bioclaw | Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Trig... |
| query-reactome | bioclaw | Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or react... |
| generate-image | kdense | Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, v... |
| scientific-schematics | kdense | Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality revi... |
| conn-tool | neuroclaw | Use this skill whenever the user wants to perform advanced functional connectivity (ROI-to-ROI, seed-to-voxel, ICA) or effective connectivity (PPI,... |
| Functional Enrichment Analysis (GSEA + ORA) | omicsclaw | Perform functional enrichment analysis using clusterProfiler on differential expression results with GSEA and ORA. |
9 skills — 16S/ITS amplicon, Kraken2, MetaPhlAn, QIIME2.
| Skill | Source | Description |
|---|---|---|
| bio-blast-searches | bioskills | Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking... |
| bio-crispr-screens-screen-qc | bioskills | Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essent... |
| bio-microbiome-qiime2-workflow | bioskills | QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when pr... |
| bio-microbiome-taxonomy-assignment | bioskills | Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact mat... |
| microbiome-cancer-agent | openclaw | AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targe... |
| meg-skill | neuroclaw | Use this skill whenever the user wants to process MEG (magnetoencephalography) data including source localization, time-frequency analysis, connect... |
| wmh-segmentation | neuroclaw | Use this skill whenever the user wants to perform automated white matter hyperintensity (WMH) segmentation on structural MRI data using the MARS-WM... |
| bio-annotation | omics | Functional annotation and taxonomy inference from sequence homology. |
| tracking-taxonomy-updates | omics | Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance. |
7 skills — RFDiffusion, ProteinMPNN, Boltz, Chai, LigandMPNN.
| Skill | Source | Description |
|---|---|---|
| bio-clip-seq-m6a-clip | bioskills | Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kor... |
| bio-tcr-bcr-analysis-immcantation-analysis | bioskills | Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. Use when studying B... |
| mage-antibody-generator | openclaw | Ab seq forge |
| ligandmpnn | adaptyv | Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site... |
| rfdiffusion | adaptyv | Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1)... |
| solublempnn | adaptyv | Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubilit... |
| generate_scientific_method_section | labclaw | Automated SCI-standard Methods section generator from experiment execution records. Parses LabOS skill call chains, structured JSON logs (extract_e... |
17 skills — Official NVIDIA BioNeMo NIM API skills for protein structure prediction, molecular generation, and genomics.
| Skill | Type | Description |
|---|---|---|
| boltz2-nim | NIM API | Boltz-2 biomolecular structure prediction via NVIDIA NIM API. |
| diffdock-nim | NIM API | DiffDock molecular docking via NVIDIA NIM API. |
| evo2-nim | NIM API | Evo2 genomic foundation model inference via NVIDIA NIM API. |
| genmol-nim | NIM API | GenMol molecule generation via NVIDIA NIM API. |
| molmim-nim | NIM API | MolMIM controlled molecular generation via NVIDIA NIM API. |
| msa-search-nim | NIM API | MSA search for protein structure prediction via NVIDIA NIM API. |
| openfold2-nim | NIM API | OpenFold2 protein structure prediction via NVIDIA NIM API. |
| openfold3-nim | NIM API | OpenFold3 biomolecular complex structure prediction via NVIDIA NIM API. |
| proteinmpnn-nim | NIM API | ProteinMPNN inverse folding / sequence design via NVIDIA NIM API. |
| rfdiffusion-nim | NIM API | RFdiffusion protein backbone design via NVIDIA NIM API. |
| proteina-complexa | Open Model | NVIDIA Proteina protein complex structure prediction. |
| kermt | Open Model | NVIDIA KERMT kernel estimation for molecular simulation. |
| cuEquivariance | Library | GPU-accelerated equivariant neural network operations. |
| genomics-workflow-acceleration | Library | Parabricks-powered GPU genomics pipeline acceleration. |
| nvMolKit | Library | NVIDIA molecular toolkit for cheminformatics and property prediction. |
| parabricks | Library | NVIDIA Parabricks GPU-accelerated GATK4 variant calling. |
| generative-protein-binder-design | Workflow | Multi-step binder design: RFdiffusion → ProteinMPNN → OpenFold3 via NIM APIs. |
Source: NVIDIA-BioNeMo/bionemo-agent-toolkit · License: Apache-2.0 (code) / CC-BY-4.0 (skills)
29 skills — Reverse-engineered Claude Science built-in skills covering biomolecular modeling, genomics, single-cell analysis, literature synthesis, and scientific compute workflows.
| Skill | Type | Description |
|---|---|---|
| alphafold2 | Structure | AlphaFold2 monomer/multimer structure prediction via ColabFold runner. |
| boltz | Structure | Boltz-2 structure prediction for protein, nucleic-acid, and small-molecule complexes. |
| chai1 | Structure | Chai-1 foundation model structure prediction for biomolecular complexes. |
| esmfold2 | Structure | ESMFold2/ESMFold2-Fast all-atom co-folding with optional MSA. |
| openfold3 | Structure | OpenFold3 open-weights PyTorch reproduction of AlphaFold3. |
| fair-esm2 | Embeddings | Meta AI ESM-2 per-residue and per-sequence protein embeddings. |
| diffdock | Docking | DiffDock-L blind diffusion-based small-molecule pose prediction. |
| ligandmpnn | Design | LigandMPNN inverse folding with ligand, nucleic-acid, and metal context. |
| proteinmpnn | Design | ProteinMPNN inverse folding from PDB backbone to amino-acid sequences. |
| solublempnn | Design | SolubleMPNN solubility-biased inverse folding for expression-friendly designs. |
| evo2 | Genomics | Evo 2 long-context genomic foundation model for scoring, embedding, and generation. |
| borzoi | Genomics | Borzoi genome-wide functional track prediction (RNA-seq, CAGE, DNase, ChIP) from DNA. |
| scgpt | Single-Cell | scGPT single-cell expression embedding and annotation with a foundation model. |
| scvi-tools | Single-Cell | scVI/scANVI probabilistic single-cell RNA-seq: batch correction, annotation, integration. |
| literature-review | Analysis | Scientific literature search, verification, and synthesis from DOI or query. |
| indication-dossier | Analysis | Therapeutic indication dossier: epidemiology, disease biology, regulatory, trials. |
| paper-narrative | Analysis | Judge and reshape the story a paper's figures tell; narrative coherence analysis. |
| pdf-explore | Analysis | Deep PDF reading with annotation, cross-referencing, and structured extraction. |
| figure-composer | Visualization | Compose publication-grade multi-panel figures from data references and claims. |
| figure-style | Visualization | Publication figure correctness and legibility rules; applies to any plot output. |
| compute-env-setup | Compute | Set up and configure remote compute environments for Claude Science jobs. |
| remote-compute-modal | Compute | Run GPU jobs on the user's Modal account via BYOC provider. |
| remote-compute-ssh | Compute | Submit→wait→harvest workflow for SSH/SLURM HPC hosts. |
| managed-model-endpoints | Compute | Register and manage local model server containers as named endpoints. |
| using-model-endpoint | Compute | Call registered model endpoints over their native HTTP API from inference kernels. |
| customize | Meta | Create and configure custom agent profiles; author new skills via the repl tool. |
| skill-creator | Meta | Create, modify, benchmark, and improve skills with eval pipeline and scoring. |
| self-awareness | Meta | Claude Science session database schema and SDK introspection surface. |
| product-self-knowledge | Meta | Authoritative Claude Science factual self-knowledge; load before answering product questions. |
Source: JimLiu/science-skills · License: Apache-2.0 · Reverse-engineered from Claude Science · Synced: fb309c3 (2026-07-01)
This collection aggregates and deduplicates skills from the following open-source repositories:
| Repository | Skills | Focus |
|---|---|---|
| GPTomics/bioSkills | 536 | Systematic bioinformatics suite from QC to multi-omics. |
| FreedomIntelligence/OpenClaw-Medical-Skills | 359 | Medical AI library aggregating 12 specialized sub-repositories. |
| jaechang-hits/SciAgent-Skills | 154 | Scientific agent skills for statistics, databases, and clinical decisions. |
| K-Dense-AI/scientific-agent-skills | 102 | General scientific computing and HPC workflow skills. |
| CUHK-AIM-Group/NeuroClaw | 86 | Neuroimaging skills: sMRI, fMRI, dMRI, EEG with BIDS, FreeSurfer, FSL, fMRIPrep. CUHK AIM Group. |
| ClawBio/ClawBio | 63 | Bioinformatics workflow orchestration for GWAS and single-cell. |
| wu-yc/LabClaw | 59 | Lab automation and biomedical research skills. Stanford-Princeton AI Co-Scientists. |
| QSong-github/DrugClaw | 57 | Drug intelligence skills: DTI, ADR, DDI, pharmacogenomics, repurposing. LangGraph-powered. |
| ChrisLou-bioinfo/nobel-medicine-minds | 55 | Cognitive frameworks of 52 Nobel Medicine laureates (2004–2025) as runnable SKILL.md files. |
| zongtingwei/Bioclaw_Skills_Hub | 46 | Ten-category biological skills hub. |
| Runchuan-BU/BioClaw | 37 | Core bioinformatics tools and database query skills. |
| fmschulz/omics-skills | 29 | Single-cell and spatial omics specialized skills. |
| TianGzlab/OmicsClaw | 28 | 6-omics domain skills: spatial, scRNA-seq, bulk RNA-seq, genomics, proteomics, metabolomics. |
| adaptyvbio/protein-design-skills | 21 | Full protein design toolkit: RFDiffusion, ProteinMPNN, Boltz, Chai. |
| aristoteleo/PantheonOS | 18 | Single-cell and spatial transcriptomics skills. Dynamo/Spateo team. |
| EvoScientist/EvoSkills | 13 | Research-lifecycle skills: ideation, paper planning, experiment execution, writing, and review. |
| xjtulyc/MedgeClaw | 7 | Biomedical research skills with real-time dashboard, RStudio, and JupyterLab integration. |
| zamushwani2/biomedical-ai-skills | 4 | Cancer multi-omics analysis skills in R. |
| ArcInstitute/SRAgent | 1 | Intelligent SRA and GEO dataset retrieval. |
| NVIDIA-BioNeMo/bionemo-agent-toolkit | 17 | Official NVIDIA BioNeMo NIM skills: Boltz-2, DiffDock, OpenFold2/3, RFdiffusion, ProteinMPNN, GenMol, Evo2, MolMIM, Parabricks. |
| JimLiu/science-skills | 29 | Reverse-engineered Claude Science built-in skills: structure prediction, design, genomics, single-cell, literature, and compute. |
| BioTender-max/awesome-bio-agent-skills | 1 | Self-referential hub skill that indexes this collection (browse & install entry point). |
Each skill is a self-contained folder with a SKILL.md file defining domain knowledge, tool usage, and expected outputs. Compatible with any Claude-based agent framework supporting the SKILL.md convention.
skills/
└── <source>/
└── <skill-name>/
├── SKILL.md # Skill definition (required)
└── ... # Supporting files
Quick install:
git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git
cp -r awesome-bio-agent-skills/skills/* /path/to/your/agent/skills/
A machine-readable index of all 1,693 skills is available in bioskill_index_v3.csv.
If this collection is useful to you, please consider giving it a ⭐ — it helps others discover it.
11 followers · starred Jun 2026
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
See the code
# One-time use (no install required)
npx bioskill install
# Or install globally for repeated use
npm install -g bioskill
bioskill install
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
Now tracking NVIDIA BioNeMo Agent Toolkit, Claude Science built-in skills, and the emerging ecosystem of agent-callable tools for life sciences.
1,722 deduplicated skills from 22 open-source repositories, organized into 16 categories. Each skill is a self-contained SKILL.md folder compatible with Claude-based agent frameworks (OpenClaw, NanoClaw, Biomni).
This project is created and maintained by BioTender.
BioTender is a Chinese AI-for-Biology intelligence and media platform covering protein design, structure prediction, virtual cells, AI drug discovery, biological foundation models, scientific agents, AI4Bio startups, and frontier research.
526 skills — WGS/WES analysis, variant annotation, GWAS, CNV, structural variants, haplotype phasing, genome assembly.
| Skill | Source | Description |
|---|---|---|
| bio-alignment-amplicon-clipping | bioskills | Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer pan... |
| bio-alignment-filtering | bioskills | Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality al... |
| bio-alignment-indexing | bioskills | Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific... |
| bio-alignment-io | bioskills | Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and othe... |
| bio-alignment-msa-parsing | bioskills | Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations,... |
| bio-alignment-msa-statistics | bioskills | Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing... |
| bio-alignment-multiple | bioskills | Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, seq... |
| bio-alignment-pairwise | bioskills | Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scorin... |
| bio-alignment-sorting | bioskills | Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end... |
| bio-alignment-structural | bioskills | Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coor... |
| bio-alignment-trimming | bioskills | Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when re... |
| bio-alignment-validation | bioskills | Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when... |
| bio-atac-seq-allele-specific-accessibility | bioskills | Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic v... |
| bio-atac-seq-atac-peak-calling | bioskills | Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligne... |
| bio-atac-seq-consensus-peakset | bioskills | Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and major... |
| bio-bam-statistics | bioskills | Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating cove... |
| bio-basecalling | bioskills | Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified b... |
| bio-bedgraph-handling | bioskills | Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization,... |
| bio-biomart-queries | bioskills | Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use... |
| bio-causal-genomics-colocalization-analysis | bioskills | Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR,... |
| bio-causal-genomics-effector-gene-prioritization | bioskills | Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021),... |
| bio-causal-genomics-fine-mapping | bioskills | Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, M... |
| bio-causal-genomics-genetic-correlation | bioskills | Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL,... |
| bio-causal-genomics-genomic-sem | bioskills | Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor... |
| bio-causal-genomics-mediation-analysis | bioskills | Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-st... |
| bio-causal-genomics-mendelian-randomization | bioskills | Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egge... |
| bio-causal-genomics-pleiotropy-detection | bioskills | Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiot... |
| bio-causal-genomics-proteome-mr-drug-target | bioskills | Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP... |
| bio-causal-genomics-transcriptome-wide-association | bioskills | Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-Mu... |
| bio-cfdna-preprocessing | bioskills | Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal usi... |
| bio-chipseq-allele-specific-binding | bioskills | Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter;... |
| bio-chipseq-chip-deep-learning | bioskills | Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft moti... |
| bio-chipseq-peak-calling | bioskills | Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size m... |
| bio-chipseq-visualization | bioskills | Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven trac... |
| bio-clinical-biostatistics-adaptive-designs | bioskills | Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Frie... |
| bio-clinical-biostatistics-categorical-tests | bioskills | Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern M... |
| bio-clinical-biostatistics-power-sample-size | bioskills | Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equ... |
| bio-clinical-databases-acmg-classification | bioskills | Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pe... |
| bio-clinical-databases-clinvar-lookup | bioskills | Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF... |
| bio-clinical-databases-dbsnp-queries | bioskills | Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build... |
...and 486 additional genomics skills in the skills/bioskills/, skills/openclaw/, skills/sciagent/ directories.
167 skills — mass spectrometry analysis, structure prediction, protein design, binding affinity optimization.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-nucleosome-positioning | bioskills | Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter.... |
| bio-data-visualization-sequence-logos | bioskills | Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability... |
| bio-generative-design | bioskills | Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based ge... |
| bio-hi-c-analysis-hic-differential | bioskills | Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significan... |
| bio-hi-c-analysis-tad-detection | bioskills | Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and... |
| bio-immunoinformatics-mhc-binding-prediction | bioskills | Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from pr... |
| bio-immunoinformatics-neoantigen-prediction | bioskills | Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient... |
| bio-interaction-databases | bioskills | Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use... |
| bio-ml-docking-rescoring | bioskills | Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity)... |
| bio-molecular-io | bioskills | Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handl... |
| bio-molecular-standardization | bioskills | Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping,... |
| bio-pdb-geometric-analysis | bioskills | Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing st... |
| bio-pdb-structure-io | bioskills | Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB,... |
| bio-pdb-structure-modification | bioskills | Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-... |
| bio-pdb-structure-navigation | bioskills | Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over st... |
| bio-phylo-tree-manipulation | bioskills | Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collap... |
| bio-population-genetics-population-structure | bioskills | Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, assess ancestry proportions,... |
| bio-pose-validation | bioskills | Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planar... |
| bio-primer-design-primer-validation | bioskills | Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complement... |
| bio-protac-degraders | bioskills | Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (l... |
| bio-proteomics-data-import | bioskills | Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Use when star... |
| bio-proteomics-dia-analysis | bioskills | Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free... |
| bio-proteomics-peptide-identification | bioskills | Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searc... |
| bio-proteomics-protein-inference | bioskills | Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles protein groups and... |
| bio-proteomics-quantification | bioskills | Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic label... |
| bio-proteomics-spectral-libraries | bioskills | Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-base... |
| bio-qsar-modeling | bioskills | Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handl... |
| bio-rna-structure-ncrna-search | bioskills | Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database. Identifies str... |
| bio-rna-structure-structure-probing | bioskills | Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucle... |
| bio-scaffold-analysis | bioskills | Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis v... |
| bio-similarity-searching | bioskills | Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules... |
| bio-structural-biology-alphafold-predictions | bioskills | Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures,... |
| bio-structural-biology-modern-structure-prediction | bioskills | Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel prot... |
| bio-substructure-search | bioskills | Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticit... |
| bio-transcription-translation | bioskills | Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using... |
| bio-virtual-screening | bioskills | Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice ru... |
| adhd-daily-planner | openclaw | Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-a... |
| alphafold-database | openclaw | Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (... |
| antibody-design-agent | openclaw | An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion). |
| bindingdb-database | openclaw | Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathoge... |
...and 127 additional proteomics skills in the skills/kdense/, skills/openclaw/, skills/sciagent/ directories.
144 skills — preprocessing, clustering, cell type annotation, trajectory inference, cell communication, multimodal integration.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-co-accessibility | bioskills | Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linki... |
| bio-atac-seq-deep-learning-atac | bioskills | Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond... |
| bio-atac-seq-enhancer-gene-linking | bioskills | Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target g... |
| bio-atac-seq-motif-deviation | bioskills | Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correl... |
| bio-atac-seq-single-cell-atac | bioskills | Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (pai... |
| bio-causal-genomics-heritability-partitioning | bioskills | Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level gen... |
| bio-chipseq-chromatin-state-segmentation | bioskills | Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate H... |
| bio-chipseq-peak-annotation | bioskills | Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPsee... |
| bio-clip-seq-stamp-antibody-free | bioskills | Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), T... |
| bio-crispr-screens-combinatorial-screens | bioskills | Designs and analyzes combinatorial CRISPR screens covering paired-Cas9 (Big Papi, Najm 2018), enhanced AsCas12a multiplex (enCas12a, DeWeirdt 2021)... |
| bio-crispr-screens-perturb-seq-analysis | bioskills | Analyzes single-cell pooled CRISPR screens (Perturb-seq, CROP-seq, Perturb-CITE-seq, ECCITE-seq, multiome) where each cell carries an sgRNA and a s... |
| bio-data-visualization-dimensionality-reduction-plots | bioskills | Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, loc... |
| bio-data-visualization-matplotlib-fundamentals | bioskills | Build publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (... |
| bio-expression-matrix-normalization | bioskills | Normalize and transform RNA-seq count matrices for differential expression, visualization, and clustering. Covers between-sample (TMM, RLE, upper q... |
| bio-expression-matrix-sparse-handling | bioskills | Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where m... |
| bio-flow-cytometry-clustering-phenotyping | bioskills | Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discover... |
| bio-flow-cytometry-doublet-detection | bioskills | Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering... |
| bio-flow-cytometry-doublet-detection | bioskills | Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering... |
| bio-gene-regulatory-networks-coexpression-networks | bioskills | Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detect... |
| bio-gene-regulatory-networks-multiomics-grn | bioskills | Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data using SCENIC+ to identify eRegulons linking tra... |
| bio-gene-regulatory-networks-scenic-regulons | bioskills | Infer gene regulatory networks and identify transcription factor regulons from single-cell RNA-seq data using pySCENIC. Discovers co-expression mod... |
| bio-imaging-mass-cytometry-cell-segmentation | bioskills | Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segme... |
| bio-imaging-mass-cytometry-interactive-annotation | bioskills | Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation val... |
| bio-imaging-mass-cytometry-phenotyping | bioskills | Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assign... |
| bio-imaging-mass-cytometry-spatial-analysis | bioskills | Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when... |
| bio-machine-learning-atlas-mapping | bioskills | Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without r... |
| bio-methylation-dmr-detection | bioskills | Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions... |
| bio-read-qc-umi-processing | bioskills | Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate... |
| bio-single-cell-batch-integration | bioskills | Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biologic... |
| bio-single-cell-cell-annotation | bioskills | Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell l... |
| bio-single-cell-cell-communication | bioskills | Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis. Use when i... |
| bio-single-cell-clustering | bioskills | Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clu... |
| bio-single-cell-data-io | bioskills | Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad... |
| bio-single-cell-doublet-detection | bioskills | Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and s... |
| bio-single-cell-doublet-detection | bioskills | Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and s... |
| bio-single-cell-lineage-tracing | bioskills | Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or d... |
| bio-single-cell-markers-annotation | bioskills | Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for differential expression between clus... |
| bio-single-cell-metabolite-communication | bioskills | Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. Predict metabolite secreti... |
| bio-single-cell-multimodal-integration | bioskills | Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA... |
| bio-single-cell-perturb-seq | bioskills | Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturb... |
...and 104 additional single-cell analysis skills in the skills/openclaw/, skills/bioskills/, skills/sciagent/ directories.
236 skills — medical AI, clinical decision support, drug discovery, general biological tools.
| Skill | Source | Description |
|---|---|---|
| bio-flow-cytometry-bead-normalization | bioskills | Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalizatio... |
| bio-flow-cytometry-fcs-handling | bioskills | Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading an... |
| bio-immunoinformatics-tcr-epitope-binding | bioskills | Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to their cognate epitope... |
| bio-molecular-descriptors | bioskills | Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descript... |
| bio-phylo-divergence-dating | bioskills | Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenie... |
| bio-phylo-species-trees | bioskills | Estimate species trees using coalescent methods including ASTRAL-III, wASTRAL, ASTRAL-Pro, SVDQuartets, and BPP. Use when multi-locus data shows ge... |
| bio-phylo-tree-io | bioskills | Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, conver... |
| bio-reporting-quarto-reports | bioskills | Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS. Use when creating... |
| bio-ribo-seq-ribosome-stalling | bioskills | Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause si... |
| aav-vector-design-agent | openclaw | AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization. |
| ai-analyzer | openclaw | AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。 |
| bayesian-optimizer | openclaw | Bayesian Optimize |
| biokernel | openclaw | Biomedical OS Core & MCP Server |
| biologist-analyst | openclaw | Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology framework... |
| biomcp-server | openclaw | MCP bio bridge |
| brainstorming | openclaw | You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user int... |
| cellagent-annotation | openclaw | Cell tagger |
| chemist-analyst | openclaw | Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectro... |
| computational-pathology-agent | openclaw | Analyze Whole Slide Images (WSI) for digital pathology, including tissue segmentation and feature extraction. |
| crisis-response-protocol | openclaw | Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or su... |
| crispr-guide-design | openclaw | Guide foundry |
| data-transform | openclaw | Transform, clean, reshape, and preprocess data using pandas and numpy. Works with ANY LLM provider (GPT, Gemini, Claude, etc.). |
| differentiation-schemes | openclaw | Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes, buildin... |
| dispatching-parallel-agents | openclaw | Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies |
| emergency-card | openclaw | 生成紧急情况下快速访问的医疗信息摘要卡片。当用户需要旅行、就诊准备、紧急情况或询问"紧急信息"、"医疗卡片"、"急救信息"时使用此技能。提取关键信息（过敏、用药、急症、植入物），支持多格式输出（JSON、文本、二维码），用于急救或快速就医。 |
| epidemiologist-analyst | openclaw | Analyzes disease patterns and health events through epidemiological lens using surveillance systems, outbreak investigation methods, and disease mo... |
| executing-plans | openclaw | Use when you have a written implementation plan to execute in a separate session with review checkpoints |
| family-health-analyzer | openclaw | 分析家族病史、评估遗传风险、识别家庭健康模式、提供个性化预防建议 |
| fhir-developer-skill | openclaw | FHIR API development guide for building healthcare endpoints. Use when: (1) Creating FHIR REST endpoints (Patient, Observation, Encounter, Conditio... |
| find-skills | openclaw | Helps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", o... |
| fitness-analyzer | openclaw | 分析运动数据、识别运动模式、评估健身进展，并提供个性化训练建议。支持与慢性病数据的关联分析。 |
| goal-analyzer | openclaw | 分析健康目标数据、识别目标模式、评估目标进度,并提供个性化目标管理建议。支持与营养、运动、睡眠等健康数据的关联分析。 |
| grief-companion | openclaw | Compassionate bereavement support, memorial creation, grief education, and healing journey guidance. Specializes in understanding grief stages, cre... |
| health-trend-analyzer | openclaw | 分析一段时间内健康数据的趋势和模式。关联药物、症状、生命体征、化验结果和其他健康指标的变化。识别令人担忧的趋势、改善情况，并提供数据驱动的洞察。当用户询问健康趋势、模式、随时间的变化或"我的健康状况有什么变化？"时使用。支持多维度分析（体重/BMI、症状、药物依从性、化验结果、情绪睡眠），相关... |
| hipaa-compliance | openclaw | Ensure HIPAA compliance when handling PHI (Protected Health Information). Use when writing code that accesses user health data, check-ins, journal... |
| kragen-knowledge-graph | openclaw | Graph-RAG Solver |
| leads-literature-mining | openclaw | Review Automator |
| medical-imaging-review | openclaw | Write comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses... |
| mental-health-analyzer | openclaw | 分析心理健康数据、识别心理模式、评估心理健康状况、提供个性化心理健康建议。支持与睡眠、运动、营养等其他健康数据的关联分析。 |
| mesh-generation | openclaw | Plan and evaluate mesh generation for numerical simulations. Use when choosing grid resolution, checking aspect ratios/skewness, estimating mesh qu... |
...and 196 additional biology and ai skills in the skills/nobel/, skills/openclaw/, skills/neuroclaw/ directories.
152 skills — EHR analysis, clinical trial design, drug interactions, precision medicine, adverse event detection.
| Skill | Source | Description |
|---|---|---|
| bio-admet-prediction | bioskills | Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handlin... |
| bio-clinical-biostatistics-bayesian-trials | bioskills | Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtur... |
| bio-clinical-biostatistics-cdisc-data | bioskills | Reads, validates, and prepares CDISC SDTM and ADaM clinical trial data for analysis. Covers SDTM domain joins (DM, AE, EX, VS, LB, DS), ADaM archit... |
| bio-clinical-biostatistics-effect-measures | bioskills | Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen,... |
| bio-clinical-biostatistics-logistic-regression | bioskills | Performs logistic regression for clinical trial outcomes (binary, ordinal, multinomial) with marginal-vs-conditional estimand reporting per FDA 202... |
| bio-clinical-biostatistics-missing-data | bioskills | Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-b... |
| bio-clinical-biostatistics-multiplicity-graphical | bioskills | Implements multiplicity control for confirmatory clinical trials using graphical procedures (Bretz-Maurer-Hommel), gatekeeping (parallel, serial, m... |
| bio-clinical-biostatistics-subgroup-analysis | bioskills | Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction t... |
| bio-clinical-biostatistics-trial-reporting | bioskills | Prepares statistical reports for clinical trials following CONSORT 2025, SPIRIT 2025, ICH E9(R1) estimands, and FDA 2023 covariate adjustment guida... |
| bio-clinical-databases-polygenic-risk | bioskills | Constructs and validates polygenic risk scores using LDpred2-auto, SBayesRC, MegaPRS, PRS-CS, PROSPER, MUSSEL, BridgePRS, JointPRS, PRSmix, or PGS... |
| bio-covalent-design | bioskills | Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartat... |
| bio-systems-biology-gene-essentiality | bioskills | Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and ide... |
| bio-workflows-clinical-trial-pipeline | bioskills | End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regula... |
| bio-workflows-outbreak-pipeline | bioskills | End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating,... |
| agentd-drug-discovery | openclaw | Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks. |
| autonomous-oncology-agent | openclaw | Precision Oncology |
| biomedical-search | openclaw | Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search. |
| cancer-metabolism-agent | openclaw | AI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilitie... |
| cart-design-optimizer-agent | openclaw | AI-guided CAR-T cell design for solid tumors using antigen prioritization, safety-by-design architectures, and exhaustion-resistant engineering. |
| cellular-senescence-agent | openclaw | AI-powered analysis of cellular senescence for aging research, cancer therapy response, and senolytic drug development. |
| chatehr-clinician-assistant | openclaw | EHR Chat Assistant |
| chematagent-drug-discovery | openclaw | Chemical Lab Agent |
| chemcrow-drug-discovery | openclaw | An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design. |
| chemical-property-lookup | openclaw | Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools. |
| chromosomal-instability-agent | openclaw | AI-powered analysis of chromosomal instability (CIN) signatures for cancer prognosis, immunotherapy response prediction, and therapeutic vulnerabil... |
| clinical-diagnostic-reasoning | openclaw | Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application. For dia... |
| clinical-trial-protocol-skill | openclaw | Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Gener... |
| clinical-trials-search | openclaw | Search ClinicalTrials.gov with natural language queries. Find clinical trials, enrollment, and outcomes using Valyu semantic search. |
| clinicaltrials-database | openclaw | Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, f... |
| ctdna-dynamics-mrd-agent | openclaw | AI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse predi... |
| cytokine-storm-analysis-agent | openclaw | AI-powered cytokine release syndrome (CRS) and cytokine storm analysis for prediction, monitoring, and management in immunotherapy and infectious d... |
| datacommons-client | openclaw | Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with d... |
| drug-discovery-search | openclaw | End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language powered by Valyu. |
| drug-interaction-checker | openclaw | Checks for potential drug-drug interactions (DDIs) between a list of medications. |
| drug-labels-search | openclaw | Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu. |
| drugbank-search | openclaw | Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu. |
| exosome-ev-analysis-agent | openclaw | AI-powered extracellular vesicle and exosome analysis for cancer biomarker discovery, liquid biopsy applications, and intercellular communication p... |
| immune-checkpoint-combination-agent | openclaw | AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular prof... |
| liquid-biopsy-analytics-agent | openclaw | Comprehensive analysis of liquid biopsy data (ctDNA, CTCs) for cancer detection, MRD monitoring, and response tracking. |
| medical-entity-extractor | openclaw | Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages. |
...and 112 additional clinical and medical skills in the skills/drugclaw/, skills/openclaw/, skills/sciagent/ directories.
97 skills — RNA-seq full pipeline, differential expression, alternative splicing, lncRNA, small RNA.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-differential-accessibility | bioskills | Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessib... |
| bio-chipseq-differential-binding | bioskills | Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices... |
| bio-chipseq-spike-in-normalization | bioskills | Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CU... |
| bio-clip-seq-ago-clip-mirna-targets | bioskills | Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (... |
| bio-clip-seq-binding-site-annotation | bioskills | Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with... |
| bio-clip-seq-differential-clip | bioskills | Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sli... |
| bio-codon-usage | bioskills | Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences... |
| bio-crispr-screens-batch-correction | bioskills | Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative... |
| bio-crispr-screens-batch-correction | bioskills | Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative... |
| bio-data-visualization-network-visualization | bioskills | Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamad... |
| bio-data-visualization-volcano-and-ma-plots | bioskills | Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement... |
| bio-de-deseq2-basics | bioskills | Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, runni... |
| bio-de-edger-basics | bioskills | Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test frame... |
| bio-de-results | bioskills | Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multipl... |
| bio-differential-expression-batch-correction | bioskills | Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting... |
| bio-differential-expression-batch-correction | bioskills | Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting... |
| bio-differential-expression-timeseries-de | bioskills | Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when... |
| bio-differential-splicing | bioskills | Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial... |
| bio-epitranscriptomics-m6a-differential | bioskills | Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or c... |
| bio-epitranscriptomics-m6a-peak-calling | bioskills | Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data. |
| bio-epitranscriptomics-m6anet-analysis | bioskills | Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read... |
| bio-expression-matrix-counts-ingest | bioskills | Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantific... |
| bio-flow-cytometry-differential-analysis | bioskills | Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testi... |
| bio-gene-regulatory-networks-differential-networks | bioskills | Compare gene regulatory and co-expression networks between biological conditions to identify rewired regulatory relationships using DiffCorr. Detec... |
| bio-gene-regulatory-networks-perturbation-simulation | bioskills | Simulate transcription factor perturbation effects on cell state using CellOracle, which integrates GRN inference with in silico knockout and overe... |
| bio-geo-data | bioskills | Query and download from NCBI Gene Expression Omnibus (GEO) and EMBL-EBI's BioStudies/ArrayExpress mirror. Use when finding expression datasets, nav... |
| bio-immunoinformatics-immunogenicity-scoring | bioskills | Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and seque... |
| bio-isoform-switching | bioskills | Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protei... |
| bio-metabolomics-statistical-analysis | bioskills | Statistical analysis for metabolomics data. Covers preprocessing (log2 transformation, normalization), limma moderated testing with empirical Bayes... |
| bio-methylation-differential-cpg | bioskills | Per-CpG differential methylation testing from bisulfite sequencing count data or beta-value matrices. Covers beta and M-value computation, coverage... |
| bio-microbiome-differential-abundance | bioskills | Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying t... |
| bio-microbiome-differential-abundance | bioskills | Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying t... |
| bio-multi-omics-mofa-integration | bioskills | Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variat... |
| bio-pathway-go-enrichment | bioskills | Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from d... |
| bio-pathway-gsea | bioskills | Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes i... |
| bio-proteomics-differential-abundance | bioskills | Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and D... |
| bio-proteomics-differential-abundance | bioskills | Statistical testing for differentially abundant proteins between conditions. Covers preprocessing (log2 transformation, normalization), limma and D... |
| bio-reverse-complement | bioskills | Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or conver... |
| bio-ribo-seq-translation-efficiency | bioskills | Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between con... |
| bio-rna-quantification-tximport-workflow | bioskills | Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when i... |
...and 57 additional transcriptomics skills in the skills/bioskills/, skills/openclaw/, skills/omicsclaw/ directories.
63 skills — UniProt, PDB, KEGG, Reactome, GEO, ClinVar, Ensembl, STRING.
| Skill | Source | Description |
|---|---|---|
| bio-batch-downloads | bioskills | Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of... |
| bio-data-visualization-ggplot2-fundamentals | bioskills | Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with... |
| bio-motif-search | bioskills | Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulat... |
| bio-restriction-sites | bioskills | Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially... |
| bio-retrosynthesis | bioskills | Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynF... |
| biomni-general-agent | openclaw | Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions. |
| biomni-research-agent | openclaw | Bio-Research Generalist |
| chembl-search | openclaw | Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search. |
| deep-research | openclaw | Execute autonomous multi-step deep research on any topic. Use when the user asks for comprehensive research, literature reviews, competitive analys... |
| deep-research-swarm | openclaw | Multi-agent research literature analysis |
| knowledge-synthesis | openclaw | Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on fres... |
| labstep | openclaw | Interact with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities. |
| literature-search | openclaw | Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search. |
| mcpmed-bioinformatics-server | openclaw | Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser. |
| medrxiv-search | openclaw | Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search. |
| nonlinear-solvers | openclaw | Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration,... |
| patents-search | openclaw | Search global patents with natural language queries. Prior art, patent landscapes, and innovation tracking via Valyu. |
| perplexity-search | openclaw | Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when condu... |
| pubmed-search | openclaw | Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks abo... |
| research-grants | openclaw | Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts... |
| research-literature | openclaw | Research Literature agent for healthcare workflows. |
| research-lookup | openclaw | Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects th... |
| scientific-problem-selection | openclaw | This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic... |
| search-strategy | openclaw | Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries... |
| virtual-lab-agent | openclaw | AI-powered virtual laboratory orchestrating multi-agent scientific research teams for autonomous hypothesis generation, experimental design, and va... |
| biorxiv-database | sciagent | Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, v... |
| geopandas-geospatial | sciagent | Geospatial vector analysis extending pandas. Read/write spatial formats (Shapefile, GeoJSON, GeoPackage, Parquet, PostGIS), CRS handling, geometric... |
| plotly-interactive-visualization | sciagent | Interactive visualization with Plotly. 40+ chart types (scatter, line, heatmap, 3D, geographic) with hover, zoom, pan. Two APIs: Plotly Express (Da... |
| pymoo | sciagent | Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve wit... |
| scikit-learn-machine-learning | sciagent | Classical ML in Python: classification, regression, clustering, dim reduction, evaluation, tuning, preprocessing pipelines. Linear models, tree ens... |
| scikit-survival-analysis | sciagent | Time-to-event modeling with scikit-survival: Cox PH (elastic net), Random Survival Forests, Boosting, SVMs for censored data. C-index, Brier, time-... |
| uspto-database | sciagent | Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; downlo... |
| eqtl-catalogue-region-fetch | clawbio | Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for ev... |
| ncbi-datasets | clawbio | Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools. |
| turingdb-graph | clawbio | Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning. |
| ukb-navigator | clawbio | Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your |
| bio-dataset-search | bioclaw | Step 3: Dataset search and task matching (数据集搜索与匹配) |
| bio-tools | bioclaw | Biology research tools reference. Always available inside agent containers. |
| aeon | kdense | This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection,... |
| citation-management | kdense | Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations... |
...and 23 additional database query skills in the skills/kdense/, skills/labclaw/, skills/omics/ directories.
69 skills — MOFA, DIABLO, single-cell multimodal, spatial transcriptomics.
| Skill | Source | Description |
|---|---|---|
| bio-clinical-biostatistics-survival-analysis | bioskills | Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival tim... |
| bio-clinical-biostatistics-survival-analysis | bioskills | Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival tim... |
| bio-machine-learning-biomarker-discovery | bioskills | Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use wh... |
| bio-machine-learning-model-validation | bioskills | Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets. Prevents data leakage and overfittin... |
| bio-machine-learning-prediction-explanation | bioskills | Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive cl... |
| bio-machine-learning-survival-analysis | bioskills | Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival mode... |
| bio-machine-learning-survival-analysis | bioskills | Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival mode... |
| bio-metabolomics-lipidomics | bioskills | Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-... |
| bio-metabolomics-metabolite-annotation | bioskills | Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when... |
| bio-metabolomics-normalization-qc | bioskills | Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use whe... |
| bio-metabolomics-targeted-analysis | bioskills | Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use w... |
| bio-multi-omics-mixomics-analysis | bioskills | Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant a... |
| bio-multi-omics-similarity-network | bioskills | Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity... |
| bio-data-visualization-specialized-omics-plots | openclaw | Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, bo... |
| biomedical-data-analysis | openclaw | Omics data forge |
| dask | openclaw | Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clu... |
| digital-twin-clinical-agent | openclaw | AI-powered patient digital twin creation for clinical trial simulation, treatment outcome prediction, and personalized medicine using real-world da... |
| ehr-fhir-integration | openclaw | Provides comprehensive tools for working with Electronic Health Records (EHR) using the HL7 FHIR standard. |
| infographics | openclaw | Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates researc... |
| labarchive-integration | openclaw | Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap... |
| latex-posters | openclaw | Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters,... |
| medea-therapeutic-discovery | openclaw | An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literat... |
| multi-search-engine | openclaw | Multi search engine integration with 17 engines (8 CN + 9 Global). Supports advanced search operators, time filters, site search, privacy engines,... |
| numerical-integration | openclaw | Select and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances, adapt... |
| opentrons-integration | openclaw | Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), lab... |
| pptx-posters | openclaw | Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX p... |
| pyzotero | openclaw | Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags... |
| seaborn | openclaw | Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attr... |
| tooluniverse-immunotherapy-response-prediction | openclaw | Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and opti... |
| tooluniverse-metabolomics | openclaw | Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (22... |
| wellally-tech | openclaw | Integrate digital health data sources (Apple Health, Fitbit, Oura Ring) and connect to WellAlly.tech knowledge base. Import external health device... |
| zarr-python | openclaw | Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific... |
| brenda-database | sciagent | BRENDA Enzyme DB SOAP/REST queries: kinetic parameters (Km, Vmax, kcat, Ki), EC classes, substrate specificity, inhibitors, cofactors, organism dat... |
| kegg-pathway-analysis | sciagent | Guide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling... |
| latex-research-posters | sciagent | Research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout, typography, color schemes, figure integration, accessibility, and QA... |
| libsbml-network-modeling | sciagent | Build, read, validate, modify SBML biological network models via the libSBML Python API. SBML Levels 1–3, reactions/kinetic laws, species, rules, F... |
| protocolsio-integration | sciagent | protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materia... |
| reactome-database | sciagent | Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis s... |
| database-access | bioclaw_hub | Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources. |
| machine-learning-for-omics | bioclaw_hub | Workflow for predictive modeling, biomarker discovery, survival modeling, and explainability over omics-derived features. |
...and 29 additional multi-omics integration skills in the skills/neuroclaw/, skills/kdense/, skills/bioclaw_hub/ directories.
86 skills — sequence analysis, BLAST, tool chains, pipeline management.
| Skill | Source | Description |
|---|---|---|
| bio-batch-processing | bioskills | Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operati... |
| bio-compressed-files | bioskills | Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexa... |
| bio-filter-sequences | bioskills | Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted record... |
| bio-flow-cytometry-compensation-transformation | bioskills | Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh t... |
| bio-flow-cytometry-gating-analysis | bioskills | Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifyi... |
| bio-fragment-analysis | bioskills | Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fra... |
| bio-fragment-analysis | bioskills | Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fra... |
| bio-hi-c-analysis-hic-data-io | bioskills | Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and... |
| bio-hi-c-analysis-matrix-operations | bioskills | Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and... |
| bio-imaging-mass-cytometry-data-preprocessing | bioskills | Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when star... |
| bio-imaging-mass-cytometry-quality-metrics | bioskills | Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality... |
| bio-primer-design-primer-basics | bioskills | Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Return... |
| bio-read-qc-quality-filtering | bioskills | Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from rea... |
| bio-restriction-enzyme-selection | bioskills | Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are comm... |
| bio-restriction-fragment-analysis | bioskills | Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis... |
| bio-restriction-fragment-analysis | bioskills | Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis... |
| bio-ribo-seq-orf-detection | bioskills | Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated... |
| bio-ribo-seq-ribosome-periodicity | bioskills | Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determini... |
| bio-seq-objects | bioskills | Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-... |
| bio-sequence-properties | bioskills | Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence compos... |
| bio-sequence-slicing | bioskills | Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence... |
| bio-sequence-statistics | bioskills | Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, genera... |
| bone-marrow-ai-agent | openclaw | AI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images. |
| chemistry-agent | openclaw | Autonomous chemical synthesis & analysis |
| coagulation-thrombosis-agent | openclaw | AI-powered analysis of coagulation disorders, thrombosis risk prediction, anticoagulation management, and platelet function assessment using machin... |
| convergence-study | openclaw | Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification |
| crisis-detection-intervention-ai | openclaw | Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols. Implements suicide ideation det... |
| data-stats-analysis | openclaw | Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY L... |
| hrv-alexithymia-expert | openclaw | Heart rate variability biometrics and emotional awareness training. Expert in HRV analysis, interoception training, biofeedback, and emotional inte... |
| jungian-psychologist | openclaw | Expert in Jungian analytical psychology, depth psychology, shadow work, archetypal analysis, dream interpretation, active imagination, addiction/re... |
| numerical-stability | openclaw | Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diag... |
| openclaw | Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Cla... | |
| performance-profiling | openclaw | Identify computational bottlenecks, analyze scaling behavior, estimate memory requirements, and receive optimization recommendations for any comput... |
| polars | openclaw | Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel... |
| scikit-survival | openclaw | Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored s... |
| statsmodels | openclaw | Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference an... |
| tooluniverse-image-analysis | openclaw | Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification,... |
| umap-learn | openclaw | UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric... |
| using-superpowers | openclaw | Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifyi... |
| usmle | openclaw | Prepare for US medical licensing exams with progress tracking, weak area analysis, question bank management, and residency match planning. |
...and 46 additional bioinformatics utilities skills in the skills/neuroclaw/, skills/sciagent/, skills/kdense/ directories.
48 skills — volcano plots, heatmaps, PCA/UMAP, interactive charts.
| Skill | Source | Description |
|---|---|---|
| bio-copy-number-copy-ratio-segmentation | bioskills | Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov... |
| bio-data-visualization-color-palettes | bioskills | Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monoton... |
| bio-data-visualization-forest-funnel-plots | bioskills | Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot... |
| bio-data-visualization-interactive-visualization | bioskills | Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animation, with awareness of curr... |
| bio-data-visualization-multipanel-figures | bioskills | Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/le... |
| bio-data-visualization-statistical-annotation | bioskills | Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with co... |
| bio-phylo-tree-visualization | bioskills | Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives. Use when creating tree figures, customizing c... |
| bio-primer-design-qpcr-primers | bioskills | Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints... |
| bio-reporting-figure-export | bioskills | Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submiss... |
| bio-reporting-rmarkdown-reports | bioskills | Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use w... |
| bio-tcr-bcr-analysis-repertoire-visualization | bioskills | Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Us... |
| bio-workflows-hic-pipeline | bioskills | End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualizatio... |
| data-visualization-expert | openclaw | Generate insightful, publication-quality visualizations from complex datasets. |
| data-viz-plots | openclaw | Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.). |
| linear-solvers | openclaw | Select and configure linear solvers for systems Ax=b in dense and sparse problems. Use when choosing direct vs iterative methods, diagnosing conver... |
| markdown-mermaid-writing | openclaw | Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishe... |
| plotly | openclaw | Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, an... |
| post-processing | openclaw | Extract, analyze, and visualize simulation output data. Use for field extraction, time series analysis, line profiles, statistical summaries, deriv... |
| pytorch-lightning | openclaw | Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipe... |
| speech-pathology-ai | openclaw | Expert speech-language pathologist specializing in AI-powered speech therapy, phoneme analysis, articulation visualization, voice disorders, fluenc... |
| vaex | openclaw | Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFra... |
| cell-figure-guide | sciagent | Cell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts, uppercase panel labels, strict... |
| general-figure-guide | sciagent | Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal... |
| matplotlib-scientific-plotting | sciagent | Low-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control o... |
| napari-image-viewer | sciagent | Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis,... |
| networkx-graph-analysis | sciagent | Graph and network analysis toolkit. Four graph types (directed, undirected, multi-edge), centrality, shortest paths, community detection, generator... |
| pyimagej-fiji-bridge | sciagent | Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Au... |
| scikit-image-processing | sciagent | Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed,... |
| statistical-significance-annotation | sciagent | Guide for annotating statistical significance (p-value asterisks) on comparison plots. Covers standard notation (ns, *, **, ***, ****), matplotlib... |
| reporting-and-figure-export | bioclaw_hub | Workflow for packaging analysis outputs into reproducible reports, clean tables, and publication-ready figure exports. |
| bio-figure-design | bioclaw | Step 6: Figure design (Figure 详细设计) |
| report-template | bioclaw | Publication-quality PDF report generation using Typst templates. Produces professional scientific reports with colored section bands, styled tables... |
| neuropixels-analysis | kdense | Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen... |
| scientific-visualization | kdense | Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, err... |
| shap | kdense | Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predict... |
| generate_cell_analysis_charts | labclaw | Domain-specialized chart generator for cell biology video analysis outputs. Consumes structured JSON from analyze_lab_video_cell_behavior or compat... |
| generate_double_column_pdf_report | labclaw | Assembles experimental data, figures, methods, and results into a journal-style double-column PDF report. Uses reportlab or PyMuPDF for programmati... |
| hand-tracking-toolkit | labclaw | Facebook Research Hand Tracking Challenge Toolkit - evaluation and visualization tools for 3D hand tracking. Supports loading HOT3D data, computing... |
| hands-3d-pose | labclaw | High-quality 3D hand pose estimation for egocentric videos from ECCV 2024 (ap229997/hands). Provides 3D joint keypoints and skeleton visualization... |
| hot3d | labclaw | HOT3D (Hand-Object 3D Dataset) by Meta Facebook - multi-view egocentric hand and object 3D tracking for Aria/Quest smart glasses. State-of-the-art... |
...and 8 additional visualization skills in the skills/omics/, skills/labclaw/, skills/medgeclaw/ directories.
38 skills — Snakemake, Nextflow, CWL, WDL.
| Skill | Source | Description |
|---|---|---|
| bio-reporting-jupyter-reports | bioskills | Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when generating automated analysis re... |
| bio-workflow-management-cwl-workflows | bioskills | Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portab... |
| bio-workflow-management-nextflow-pipelines | bioskills | Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building p... |
| bio-workflow-management-snakemake-workflows | bioskills | Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-ba... |
| bio-workflow-management-wdl-workflows | bioskills | Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GAT... |
| bio-workflows-crispr-editing-pipeline | bioskills | End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and special... |
| bio-workflows-cytometry-pipeline | bioskills | End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and stati... |
| bio-workflows-imc-pipeline | bioskills | End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyp... |
| biomaster-workflows | openclaw | Pipeline maestro |
| care-coordination | openclaw | Care Coordination agent for healthcare workflows. |
| claims-appeals | openclaw | Claims Appeals agent for healthcare workflows. |
| fhir-development | openclaw | FHIR Development agent for healthcare workflows. |
| instrument-data-to-allotrope | openclaw | Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill w... |
| lab-results | openclaw | Lab Results agent for healthcare workflows. |
| pdf-processing-pro | openclaw | Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in productio... |
| pylabrobot | openclaw | Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipm... |
| regulatory-drafting | openclaw | Regulatory Drafting agent for healthcare workflows. |
| scikit-learn | openclaw | Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (cluste... |
| simulation-orchestrator | openclaw | Orchestrate multi-simulation campaigns including parameter sweeps, batch jobs, and result aggregation. Use for running parameter studies, managing... |
| single-trajectory-analysis | openclaw | Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks. |
| histolab-wsi-processing | sciagent | WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep... |
| nextflow-workflow-engine | sciagent | Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLU... |
| pylabrobot | sciagent | Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without v... |
| spikeinterface-electrophysiology | sciagent | Unified Python framework for extracellular electrophysiology. Load 20+ formats (SpikeGLX, OpenEphys, NWB, Intan, Maxwell, Blackrock), preprocess, r... |
| sequence-and-format-io | bioclaw_hub | Workflow for foundational sequence parsing, conversion, compression handling, and interval-aware file validation. |
| bioconductor-bridge | clawbio | Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded |
| bio-manuscript-pipeline | bioclaw | End-to-end pipeline from structured research input to a full manuscript plan (一条龙 Pipeline) |
| skills-hub | bioclaw | Browse and install community skills from the BioClaw Skills Hub. Use when a user's task is not covered by built-in skills, or when the user asks ab... |
| polars | kdense | Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel... |
| pydicom | kdense | Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying me... |
| scikit-survival | kdense | Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored s... |
| experiment-pipeline | evoskills | Guides structured 4-stage experiment execution with attempt budgets and gate conditions: Stage 1 initial implementation (reproduce baseline), Stage... |
| biomed-dispatch | medgeclaw | Dispatch biomedical research and data analysis tasks to Claude Code with K-Dense Scientific Skills. Use this skill when the user asks to run any bi... |
| git-workflows | neuroclaw | Advanced git operations beyond add/commit/push. Use when rebasing, bisecting bugs, using worktrees for parallel development, recovering with reflog... |
| hcppipeline-tool | neuroclaw | Use this skill whenever the user wants to perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion)... |
| bio-workflow-methods-docwriter | omics | Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, Q... |
| Gene Panel Selection Workflow | pantheon | End-to-end workflow for gene panel design in scRNA-seq and spatial transcriptomics, that should be STRICTLY followed: dataset understanding + s... |
| nf-core Pipelines Skills Index | pantheon | Skills for using nf-core community pipelines to process omics data, from installation and configuration to running specific analysis pipelines. |
19 skills — ChIP-seq, ATAC-seq, DNA methylation, Hi-C, chromatin state.
| Skill | Source | Description |
|---|---|---|
| bio-atac-seq-atac-qc | bioskills | ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, an... |
| bio-atac-seq-footprinting | bioskills | Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites w... |
| bio-chipseq-cut-and-run-tag | bioskills | Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375... |
| bio-chipseq-motif-analysis | bioskills | Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo,... |
| bio-chipseq-qc | bioskills | Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC... |
| bio-chipseq-super-enhancers | bioskills | Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing. Han... |
| bio-clip-seq-clip-motif-analysis | bioskills | Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-register... |
| bio-clip-seq-clip-qc | bioskills | Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate rep... |
| bio-copy-number-recurrent-cnv | bioskills | Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-leve... |
| bio-hi-c-analysis-compartment-analysis | bioskills | Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments f... |
| bio-hi-c-analysis-loop-calling | bioskills | Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops a... |
| bio-long-read-sequencing-nanopore-methylation | bioskills | Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from n... |
| bio-methylation-based-detection | bioskills | Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific me... |
| pptx | openclaw | Presentation creation, editing, and analysis. When Claude needs to work with presentations (.pptx files) for: (1) Creating new presentations, (2) M... |
| methylation-clock | clawbio | Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files. |
| methylation-cycle | clawbio | Methylation cycle analysis skill for ClawBio. Produces enzymatic activity |
| atac-seq | bioclaw | ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up. |
| chip-seq | bioclaw | ChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review. |
| open-notebook | kdense | Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials int... |
15 skills — KEGG, Reactome, GO, GSEA.
| Skill | Source | Description |
|---|---|---|
| bio-pathway-enrichment-visualization | bioskills | Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers... |
| bio-pathway-kegg-pathways | bioskills | KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways... |
| bio-pathway-reactome | bioskills | Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Perf... |
| bio-pathway-wikipathways | bioskills | WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Perf... |
| gsea-enrichment-analysis | openclaw | Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVe... |
| ontology-explorer | openclaw | Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, underst... |
| ontology-mapper | openclaw | Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registered in on... |
| ontology-validator | openclaw | Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, verifying... |
| tooluniverse-gene-enrichment | openclaw | Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supp... |
| query-kegg | bioclaw | Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Trig... |
| query-reactome | bioclaw | Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or react... |
| generate-image | kdense | Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, v... |
| scientific-schematics | kdense | Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality revi... |
| conn-tool | neuroclaw | Use this skill whenever the user wants to perform advanced functional connectivity (ROI-to-ROI, seed-to-voxel, ICA) or effective connectivity (PPI,... |
| Functional Enrichment Analysis (GSEA + ORA) | omicsclaw | Perform functional enrichment analysis using clusterProfiler on differential expression results with GSEA and ORA. |
9 skills — 16S/ITS amplicon, Kraken2, MetaPhlAn, QIIME2.
| Skill | Source | Description |
|---|---|---|
| bio-blast-searches | bioskills | Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. Use when identifying unknown sequences, finding homologs, picking... |
| bio-crispr-screens-screen-qc | bioskills | Quality control for pooled CRISPR screens covering library representation, Gini index, log-skew, replicate Pearson and Spearman concordance, essent... |
| bio-microbiome-qiime2-workflow | bioskills | QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when pr... |
| bio-microbiome-taxonomy-assignment | bioskills | Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact mat... |
| microbiome-cancer-agent | openclaw | AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targe... |
| meg-skill | neuroclaw | Use this skill whenever the user wants to process MEG (magnetoencephalography) data including source localization, time-frequency analysis, connect... |
| wmh-segmentation | neuroclaw | Use this skill whenever the user wants to perform automated white matter hyperintensity (WMH) segmentation on structural MRI data using the MARS-WM... |
| bio-annotation | omics | Functional annotation and taxonomy inference from sequence homology. |
| tracking-taxonomy-updates | omics | Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance. |
7 skills — RFDiffusion, ProteinMPNN, Boltz, Chai, LigandMPNN.
| Skill | Source | Description |
|---|---|---|
| bio-clip-seq-m6a-clip | bioskills | Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kor... |
| bio-tcr-bcr-analysis-immcantation-analysis | bioskills | Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. Use when studying B... |
| mage-antibody-generator | openclaw | Ab seq forge |
| ligandmpnn | adaptyv | Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site... |
| rfdiffusion | adaptyv | Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1)... |
| solublempnn | adaptyv | Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubilit... |
| generate_scientific_method_section | labclaw | Automated SCI-standard Methods section generator from experiment execution records. Parses LabOS skill call chains, structured JSON logs (extract_e... |
17 skills — Official NVIDIA BioNeMo NIM API skills for protein structure prediction, molecular generation, and genomics.
| Skill | Type | Description |
|---|---|---|
| boltz2-nim | NIM API | Boltz-2 biomolecular structure prediction via NVIDIA NIM API. |
| diffdock-nim | NIM API | DiffDock molecular docking via NVIDIA NIM API. |
| evo2-nim | NIM API | Evo2 genomic foundation model inference via NVIDIA NIM API. |
| genmol-nim | NIM API | GenMol molecule generation via NVIDIA NIM API. |
| molmim-nim | NIM API | MolMIM controlled molecular generation via NVIDIA NIM API. |
| msa-search-nim | NIM API | MSA search for protein structure prediction via NVIDIA NIM API. |
| openfold2-nim | NIM API | OpenFold2 protein structure prediction via NVIDIA NIM API. |
| openfold3-nim | NIM API | OpenFold3 biomolecular complex structure prediction via NVIDIA NIM API. |
| proteinmpnn-nim | NIM API | ProteinMPNN inverse folding / sequence design via NVIDIA NIM API. |
| rfdiffusion-nim | NIM API | RFdiffusion protein backbone design via NVIDIA NIM API. |
| proteina-complexa | Open Model | NVIDIA Proteina protein complex structure prediction. |
| kermt | Open Model | NVIDIA KERMT kernel estimation for molecular simulation. |
| cuEquivariance | Library | GPU-accelerated equivariant neural network operations. |
| genomics-workflow-acceleration | Library | Parabricks-powered GPU genomics pipeline acceleration. |
| nvMolKit | Library | NVIDIA molecular toolkit for cheminformatics and property prediction. |
| parabricks | Library | NVIDIA Parabricks GPU-accelerated GATK4 variant calling. |
| generative-protein-binder-design | Workflow | Multi-step binder design: RFdiffusion → ProteinMPNN → OpenFold3 via NIM APIs. |
Source: NVIDIA-BioNeMo/bionemo-agent-toolkit · License: Apache-2.0 (code) / CC-BY-4.0 (skills)
29 skills — Reverse-engineered Claude Science built-in skills covering biomolecular modeling, genomics, single-cell analysis, literature synthesis, and scientific compute workflows.
| Skill | Type | Description |
|---|---|---|
| alphafold2 | Structure | AlphaFold2 monomer/multimer structure prediction via ColabFold runner. |
| boltz | Structure | Boltz-2 structure prediction for protein, nucleic-acid, and small-molecule complexes. |
| chai1 | Structure | Chai-1 foundation model structure prediction for biomolecular complexes. |
| esmfold2 | Structure | ESMFold2/ESMFold2-Fast all-atom co-folding with optional MSA. |
| openfold3 | Structure | OpenFold3 open-weights PyTorch reproduction of AlphaFold3. |
| fair-esm2 | Embeddings | Meta AI ESM-2 per-residue and per-sequence protein embeddings. |
| diffdock | Docking | DiffDock-L blind diffusion-based small-molecule pose prediction. |
| ligandmpnn | Design | LigandMPNN inverse folding with ligand, nucleic-acid, and metal context. |
| proteinmpnn | Design | ProteinMPNN inverse folding from PDB backbone to amino-acid sequences. |
| solublempnn | Design | SolubleMPNN solubility-biased inverse folding for expression-friendly designs. |
| evo2 | Genomics | Evo 2 long-context genomic foundation model for scoring, embedding, and generation. |
| borzoi | Genomics | Borzoi genome-wide functional track prediction (RNA-seq, CAGE, DNase, ChIP) from DNA. |
| scgpt | Single-Cell | scGPT single-cell expression embedding and annotation with a foundation model. |
| scvi-tools | Single-Cell | scVI/scANVI probabilistic single-cell RNA-seq: batch correction, annotation, integration. |
| literature-review | Analysis | Scientific literature search, verification, and synthesis from DOI or query. |
| indication-dossier | Analysis | Therapeutic indication dossier: epidemiology, disease biology, regulatory, trials. |
| paper-narrative | Analysis | Judge and reshape the story a paper's figures tell; narrative coherence analysis. |
| pdf-explore | Analysis | Deep PDF reading with annotation, cross-referencing, and structured extraction. |
| figure-composer | Visualization | Compose publication-grade multi-panel figures from data references and claims. |
| figure-style | Visualization | Publication figure correctness and legibility rules; applies to any plot output. |
| compute-env-setup | Compute | Set up and configure remote compute environments for Claude Science jobs. |
| remote-compute-modal | Compute | Run GPU jobs on the user's Modal account via BYOC provider. |
| remote-compute-ssh | Compute | Submit→wait→harvest workflow for SSH/SLURM HPC hosts. |
| managed-model-endpoints | Compute | Register and manage local model server containers as named endpoints. |
| using-model-endpoint | Compute | Call registered model endpoints over their native HTTP API from inference kernels. |
| customize | Meta | Create and configure custom agent profiles; author new skills via the repl tool. |
| skill-creator | Meta | Create, modify, benchmark, and improve skills with eval pipeline and scoring. |
| self-awareness | Meta | Claude Science session database schema and SDK introspection surface. |
| product-self-knowledge | Meta | Authoritative Claude Science factual self-knowledge; load before answering product questions. |
Source: JimLiu/science-skills · License: Apache-2.0 · Reverse-engineered from Claude Science · Synced: fb309c3 (2026-07-01)
This collection aggregates and deduplicates skills from the following open-source repositories:
| Repository | Skills | Focus |
|---|---|---|
| GPTomics/bioSkills | 536 | Systematic bioinformatics suite from QC to multi-omics. |
| FreedomIntelligence/OpenClaw-Medical-Skills | 359 | Medical AI library aggregating 12 specialized sub-repositories. |
| jaechang-hits/SciAgent-Skills | 154 | Scientific agent skills for statistics, databases, and clinical decisions. |
| K-Dense-AI/scientific-agent-skills | 102 | General scientific computing and HPC workflow skills. |
| CUHK-AIM-Group/NeuroClaw | 86 | Neuroimaging skills: sMRI, fMRI, dMRI, EEG with BIDS, FreeSurfer, FSL, fMRIPrep. CUHK AIM Group. |
| ClawBio/ClawBio | 63 | Bioinformatics workflow orchestration for GWAS and single-cell. |
| wu-yc/LabClaw | 59 | Lab automation and biomedical research skills. Stanford-Princeton AI Co-Scientists. |
| QSong-github/DrugClaw | 57 | Drug intelligence skills: DTI, ADR, DDI, pharmacogenomics, repurposing. LangGraph-powered. |
| ChrisLou-bioinfo/nobel-medicine-minds | 55 | Cognitive frameworks of 52 Nobel Medicine laureates (2004–2025) as runnable SKILL.md files. |
| zongtingwei/Bioclaw_Skills_Hub | 46 | Ten-category biological skills hub. |
| Runchuan-BU/BioClaw | 37 | Core bioinformatics tools and database query skills. |
| fmschulz/omics-skills | 29 | Single-cell and spatial omics specialized skills. |
| TianGzlab/OmicsClaw | 28 | 6-omics domain skills: spatial, scRNA-seq, bulk RNA-seq, genomics, proteomics, metabolomics. |
| adaptyvbio/protein-design-skills | 21 | Full protein design toolkit: RFDiffusion, ProteinMPNN, Boltz, Chai. |
| aristoteleo/PantheonOS | 18 | Single-cell and spatial transcriptomics skills. Dynamo/Spateo team. |
| EvoScientist/EvoSkills | 13 | Research-lifecycle skills: ideation, paper planning, experiment execution, writing, and review. |
| xjtulyc/MedgeClaw | 7 | Biomedical research skills with real-time dashboard, RStudio, and JupyterLab integration. |
| zamushwani2/biomedical-ai-skills | 4 | Cancer multi-omics analysis skills in R. |
| ArcInstitute/SRAgent | 1 | Intelligent SRA and GEO dataset retrieval. |
| NVIDIA-BioNeMo/bionemo-agent-toolkit | 17 | Official NVIDIA BioNeMo NIM skills: Boltz-2, DiffDock, OpenFold2/3, RFdiffusion, ProteinMPNN, GenMol, Evo2, MolMIM, Parabricks. |
| JimLiu/science-skills | 29 | Reverse-engineered Claude Science built-in skills: structure prediction, design, genomics, single-cell, literature, and compute. |
| BioTender-max/awesome-bio-agent-skills | 1 | Self-referential hub skill that indexes this collection (browse & install entry point). |
Each skill is a self-contained folder with a SKILL.md file defining domain knowledge, tool usage, and expected outputs. Compatible with any Claude-based agent framework supporting the SKILL.md convention.
skills/
└── <source>/
└── <skill-name>/
├── SKILL.md # Skill definition (required)
└── ... # Supporting files
Quick install:
git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git
cp -r awesome-bio-agent-skills/skills/* /path/to/your/agent/skills/
A machine-readable index of all 1,693 skills is available in bioskill_index_v3.csv.
If this collection is useful to you, please consider giving it a ⭐ — it helps others discover it.
11 followers · starred Jun 2026