bioinformatics-agent-skills

Agent Skills for computational biology — RNA-seq, single-cell, protein structure, molecular dynamics, peptide design, literature mining and publication figures. Turn any AI coding agent into a computational biology assistant.

New — Created in the last 30 days
Active — Updated in the last 14 days

Works with

Claude

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17 skills (17 skills found in its SKILL.md files)
1 forks (1 forks)
4d ago last update (Last updated 4d ago)

Install

Skills CLI

npx skills add ssinder/bioinformatics-agent-skills

Asks which skills and agents to install. Just one: npx skills add ssinder/bioinformatics-agent-skills --skill alphafold-db — add -g for every project.

Claude Code

git clone https://github.com/ssinder/bioinformatics-agent-skillscp -r "bioinformatics-agent-skills/skills/alphafold-db" ~/.claude/skills/

Copies the alphafold-db skill into ~/.claude/skills/ for every project (use .claude/skills/ for one project). Repeat for the other skills listed below.

Plugin

/plugin marketplace add ssinder/bioinformatics-agent-skills

Run inside Claude Code if the repository ships a plugin marketplace, then pick plugins from /plugin.

Skills can run code on your machine — read the SKILL.md first.

What it does

Filter skills

In the author's own words, from each skill's SKILL.md.

alphafold-db

Downloads predicted protein structures from the EBI AlphaFold Database API and exports per-protein prediction metadata. Resolves the current PDB/CIF download URL from the API instead of hard-coding a model version, supports batch accession lists, resumable downloads, pLDDT-based quality filtering before spending bandwidth, and validates response content types so HTML error pages are never mistake…
skills/alphafold-db/SKILL.md on GitHub (opens in a new tab)
bio-database-fetch

Fetches compound properties and species taxonomy from the official PubChem PUG-REST and NCBI Taxonomy APIs. Retrieves molecular formula, weight, SMILES, InChI, InChIKey, IUPAC name, XLogP, TPSA and CAS numbers for a batch of PubChem CIDs, and full lineage classification (domain through species) for a batch of NCBI Taxonomy IDs. Supports batched queries (100 IDs per request), CSV/JSON export, and…
skills/bio-database-fetch/SKILL.md on GitHub (opens in a new tab)
bioproject-search

Retrieves NCBI BioProject metadata — title, description, organism, submitter and release dates — for a batch of BioProject accessions, using the official NCBI E-utilities API rather than scraping the BioProject web pages. Supports keyword filtering over titles and descriptions, CSV/JSON export, and requires a contact email as the NCBI usage policy mandates. This skill should be used when looking…
skills/bioproject-search/SKILL.md on GitHub (opens in a new tab)
bulk-rnaseq

This skill should be used when running bulk RNA-seq differential expression analysis: FastQC/trimming, Salmon quantification, counts matrix construction, DESeq2 statistics, GO/KEGG enrichment and publication figures. 用于 bulk 转录组（RNA-seq）差异表达分析全流程。
skills/bulk-rnaseq/SKILL.md on GitHub (opens in a new tab)
ena-download

Downloads RNA-seq and other sequencing FASTQ data from the ENA (European Nucleotide Archive) Portal API and exports run-level metadata. Resolves download URLs and file sizes from the structured API rather than scraping archive web pages, supports batch accession lists, HTTP Range resume for interrupted transfers, and MD5 verification against the checksums ENA publishes. This skill should be used…
skills/ena-download/SKILL.md on GitHub (opens in a new tab)
literature-search

This skill should be used when mining academic literature from PubMed, OpenAlex or Semantic Scholar — searching papers by topic or keywords, deduplicating multi-source results, filtering by relevance or citation count, enriching missing abstracts, and exporting RIS, BibTeX or GB/T 7714 citations. 用于多源学术文献检索、去重、相关性筛选、摘要富集与参考文献格式导出的场景。
skills/literature-search/SKILL.md on GitHub (opens in a new tab)
ml-peptide-generation

Generates candidate binder peptides for a target protein using the PepMLM-650M masked language model — appends <mask> tokens to the target sequence and samples amino acids at each position, with illegal residues (X, B, Z) excluded from the sampling candidates. Reports pseudo-perplexity for each candidate, supports reproducible generation via an explicit random seed, and provides offline filtering…
skills/ml-peptide-generation/SKILL.md on GitHub (opens in a new tab)
molecular-dynamics

Analyses molecular-dynamics trajectories with a self-contained pure-numpy DCD and PDB trajectory parser plus built-in Kabsch-Sander alignment, SVD-based PCA, hierarchical clustering of RMSD matrices, geometric hydrogen-bond detection, RMSF, radius of gyration, Ramachandran analysis, inter-chain contacts and Shrake-Rupley SASA. This skill should be used when trajectory RMSD or RMSF, PCA, conformat…
skills/molecular-dynamics/SKILL.md on GitHub (opens in a new tab)
paper-fulltext-extract

This skill should be used when extracting structured full text from scientific PDF papers — converting PDFs to TEI XML via a local GROBID service, parsing titles, authors, abstracts, keywords, section trees, figures and references into JSON, Markdown or HTML, building a searchable corpus index across many papers, and pulling the first sentences of each Introduction paragraph for rapid paper triag…
skills/paper-fulltext-extract/SKILL.md on GitHub (opens in a new tab)
peptide-design

This skill should be used when analyzing or designing antimicrobial peptides — computing physicochemical properties such as molecular weight, isoelectric point, Kyte-Doolittle hydrophobicity and instability index, classifying peptides as antimicrobial or non-antimicrobial from GO terms and sequence features, deduplicating peptide libraries by clustering, and exporting FASTA or CSV. 用于多肽理化性质计算、抗菌肽…
skills/peptide-design/SKILL.md on GitHub (opens in a new tab)
protein-docking-hdock

Submits protein-protein docking jobs to the HDOCK server and retrieves the resulting Docking Score, Confidence Score, ligand RMSD and ranked complex models. Uses plain HTTP form submission against the HDOCK server rather than browser automation, supports PDB files, PDB ID:ChainID references and FASTA sequences for both receptor and ligand, records submitted jobs to a CSV so results can be collect…
skills/protein-docking-hdock/SKILL.md on GitHub (opens in a new tab)
protein-docking-lightdock

Runs LightDock protein-protein docking locally by driving the lightdock3_setup.py and lightdock3.py executables, then extracts the best docked complex. Parses the GSO swarm output files with the correct field semantics (glowworm id is the line number, not the LigID column), selects the latest gso_<step>.out by numeric step rather than dictionary order, and generates conformations from the origin-…
skills/protein-docking-lightdock/SKILL.md on GitHub (opens in a new tab)
protein-interactions

Analyzes protein-ligand and protein-protein interactions from PLIP XML reports and AlphaFold model packages using a self-contained standard-library XML parser: extracts residue-level salt bridges, hydrogen bonds, hydrophobic, pi-stacking, water bridges, halogen bonds and metal complexes, ranks hotspot residues, and emits Mermaid network graphs plus PyMOL annotation scripts. This skill should be u…
skills/protein-interactions/SKILL.md on GitHub (opens in a new tab)
protein-structure

Analyzes protein structures from PDB files: parses ATOM/HETATM records with a dependency-free pure-Python parser, computes radius of gyration, gyration tensor and dipole moments, assigns secondary structure via DSSP or a built-in Kabsch-Sander hydrogen-bond implementation, and optionally retrieves UniProt metadata. This skill should be used when secondary structure assignment, Rg, shape analysis,…
skills/protein-structure/SKILL.md on GitHub (opens in a new tab)
pymol-structure-visualization

This skill should be used when analyzing inter-chain contacts in protein structures — computing residue-level contact geometry from PDB files with a uniform-grid spatial index, classifying each contact into hydrogen bonds, salt bridges, hydrophobic contacts, pi-pi stacking and cation-pi interactions using residue chemistry, identifying hotspot residues, and exporting CSV/JSON results together wit…
skills/pymol-structure-visualization/SKILL.md on GitHub (opens in a new tab)
scientific-figures

This skill should be used when generating publication-ready scientific figures — ROC curves, confusion matrix heatmaps, docking binding-energy heatmaps, pLDDT confidence histograms, SHAP summary beeswarms, class distribution charts and other chart types with a unified journal-grade visual style. 用于生成顶刊级出版图表（ROC 曲线、混淆矩阵、热图、pLDDT 分布、SHAP 摘要等）的场景。
skills/scientific-figures/SKILL.md on GitHub (opens in a new tab)
single-cell-rnaseq

This skill should be used when running single-cell RNA-seq analysis: reading 10x/AnnData matrices, QC filtering, normalization, HVG selection, PCA, clustering, UMAP/t-SNE and cell type annotation. 用于单细胞转录组（scRNA-seq）质控、降维、聚类与细胞注释全流程。
skills/single-cell-rnaseq/SKILL.md on GitHub (opens in a new tab)

Review before you install

A skill is a set of instructions and scripts your agent will follow, and it can run code on your machine. Read the SKILL.md and any scripts first — this listing is not a security review.

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bioinformatics-agent-skills