VoltAgent/awesome-openclaw-skillsCollections
The awesome collection of OpenClaw skills. 5,400+ skills filtered and categorized from the official OpenClaw Skills Registry.🦞
52k
Curated bio agent skills for Claude Code and agents
This repo collects 1,722 deduplicated skills for biomedical research workflows and groups them by domain. Each skill is packaged as a self-contained `SKILL.md` folder, so builders can add specific capabilities to their agent setup instead of starting from scratch.
176 stars•31 forks•Python•Updated 2mo ago
Who it's for
Builders who want reusable biomedical skills for Claude Code and other agent runtimes.
What it delivers
You can add ready-made bio research skills to your agent instead of writing each workflow by hand.
What it does
Large bio skill catalog
Indexes 1,722 skills across genomics, proteomics, single-cell analysis, clinical AI, transcriptomics, and protein design.
Source-based organization
Groups skills by topic and source repositories, with categories like `skills/bioskills/`, `skills/openclaw/`, and `skills/sciagent/`.
Claude-compatible skill packs
Packages skills as self-contained `SKILL.md` folders for Claude-based agent frameworks and similar setups.
Installable bioskill tool
Provides `bioskill` commands for installing the collection from npm.
Curated reference files
Includes CSV indexes and a zip archive for browsing or reusing the skill collection.
How to get it
- 1Run
# One-time use (no install required) npx bioskill install # Or install globally for repeated use npm install -g bioskill bioskill install
- 2Each skill is a self-contained folder with a SKILL.md file defining domain knowledge,…
skills/ └── <source>/ └── <skill-name>/ ├── SKILL.md # Skill definition (required) └── ... # Supporting files - 3Quick 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/
README
# One-time use (no install required)
npx bioskill install
# Or install globally for repeated use
npm install -g bioskill
bioskill install
Awesome Bio Agent Skills
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).
About BioTender
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.
- Website: https://www.biotender.online/
- About: https://www.biotender.online/about/
- Scholar Program: https://www.biotender.online/scholar-program.html
Contents
- Genomics
- Proteomics
- Single-Cell Analysis
- Biology and AI
- Clinical and Medical
- Transcriptomics
- Database Query
- Multi-Omics Integration
- Bioinformatics Utilities
- Visualization
- Workflow Orchestration
- Epigenomics
- Pathway Analysis
- Metagenomics
- Protein Design
- NVIDIA BioNeMo Skills
- Claude Science Skills
- Sources
Genomics
526 skills — WGS/WES analysis, variant annotation, GWAS, CNV, structural variants, haplotype phasing, genome assembly.
View all 526 skills
| 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.
Proteomics
167 skills — mass spectrometry analysis, structure prediction, protein design, binding affinity optimization.
View all 167 skills
| 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.
Single-Cell Analysis
144 skills — preprocessing, clustering, cell type annotation, trajectory inference, cell communication, multimodal integration.
View all 144 skills
| Skill | Source | Description |
|---|---|---|
| [bi |
Files in the repo
Repository payload•11 top-level entries
- .github
- assets
- docs
- skills
- bioskill_collection_v3.zip
- bioskill_index_v2.csv
- bioskill_index_v3.csv
- code-of-conduct.md
- contributing.md
- LICENSE
- README.md
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