Bioinformatics

Runs flux balance analysis and related constraint-based simulations on a COBRApy metabolic model, from standard FBA to gene knockouts and carbon source swaps.

aiming-lab/AutoResearchClaw

Make RNAlysis code faster while proving the output does not change.

GuyTeichman/RNAlysis

Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools.

davila7/claude-code-templates

A skill your agent uses when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs, or comparing CPU and GPU…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis.

davila7/claude-code-templates

Statistical analysis and reporting for single-cell RNA-seq data.

harrisongzhang/TheVirtualBiotech

200以上のファイル形式に対応した探索的データ分析（EDA）スキル. An agent skill from minicoohei/ai-agent-camp.

minicoohei/ai-agent-camp

Maintain gbdraw Web Gallery tutorial screenshots, manual text, and structured tutorial content.

satoshikawato/gbdraw

Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.

davila7/claude-code-templates

Guides your agent through building, editing, comparing and drawing phylogenetic trees with the ETE Python toolkit, including orthology calls and NCBI taxonomy lookups.

davila7/claude-code-templates

Works with genomic intervals using gtars, a Rust toolkit with Python bindings: overlap detection, coverage tracks, tokenization for ML models and reference sequences.

davila7/claude-code-templates

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data.

davila7/claude-code-templates

Python interface to OpenMS for mass spectrometry data analysis.

davila7/claude-code-templates

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…

davila7/claude-code-templates

This skill should be used when working with genomic interval data (BED files) for machine learning tasks.

davila7/claude-code-templates

This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities.

davila7/claude-code-templates

Visium HD platform branch of the spatial transcriptomics workflow — reconstruct single cells from 2 μm bins via morphological segmentation and bin-to-cell aggregation.

QING1105/ezST

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.

aipoch/medical-research-skills

Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML).

LeonChaoX/qinyan-academic-skills

Soft- or hard-clips PCR primer footprints from aligned amplicon BAMs so primer bases stop masquerading as confirmed reference sequence.

GPTomics/bioSkills

Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.

LigphiDonk/Oh-my--paper

Critically review, score, compare, and rank one or more AI scientist outputs for biology, bioinformatics, computational life science, or adjacent research tasks.

BioTender-max/awesome-bio-agent-skills

A skill your agent uses when working on bioinformatics workflows such as alignment, variant calling, phylogenetics, or protein-structure analysis, especially across BLAST, minimap2, samtools…

ZimoLiao/scholaraio

Primary Python tool for 40+ bioinformatics services. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Access COSMIC cancer mutation database. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Query Ensembl genome database REST API for 250+ species. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports.

wu-yc/LabClaw

Turns raw flux balance analysis output and a COBRApy model into gene essentiality maps, phenotypic phase planes, flux sampling results, pathway summaries and secretion predictions.

aiming-lab/AutoResearchClaw

Biological data toolkit. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and…

maziyarpanahi/openmed

Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified.

ClawBio/ClawBio

Single-cell RNA-seq data preparation and quality control pipeline.

harrisongzhang/TheVirtualBiotech

Primary Python toolkit for molecular biology. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Strategies for scientific computing, numerical methods, bioinformatics/DNA tasks, logic circuit design, algorithmic challenges, and ML training tasks.

A-EVO-Lab/a-evolve

Filters BAM alignments by FLAG bits, mapping quality and regions with samtools view or pysam, with recipes for common keep and drop cases.

GPTomics/bioSkills

CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

DNAnexus cloud genomics platform. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Query CZ CELLxGENE Census (61M+ cells). An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Latch platform for bioinformatics workflows. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Gene regulatory network workflow guide for transcriptomics and single-cell expression matrices using Arboreto, GRNBoost2, and GENIE3.

DrugClaw/DrugClaw

Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.

TianGzlab/OmicsClaw

Access European Nucleotide Archive via API/FTP. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Query NHGRI-EBI GWAS Catalog for SNP-trait associations. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Query NCBI ClinVar for variant clinical significance. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Genomic file toolkit. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Access 1000+ scientific tools through ToolUniverse for drug discovery, protein analysis, genomics, literature search, clinical data, ADMET prediction, molecular docking, and more.

AgentTeam-TaichuAI/ScienceClaw

Runs quality control on a COBRApy genome-scale metabolic model before flux analysis, checking mass and charge balance, biomass feasibility, dead ends, thermodynamic loops and GPR rules.

aiming-lab/AutoResearchClaw

Query the ENCODE Registry of cis-Regulatory Elements (cCREs) via the SCREEN GraphQL API, or make custom queries to the ENCODE Portal REST API for experiments and files (ChIP-seq peaks, etc.).

google-deepmind/science-skills