Python · Bioinformatics

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.

google-deepmind/science-skills

Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.

K-Dense-AI/scientific-agent-skills

A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.

xuzhougeng/wisp-science

Generate sashimi-style genome visualization plots (coverage, line, heatmap, IGV read-by-read, HiC, circRNA, motif) from BAM/bigWig/depth/HiC inputs.

ygidtu/trackplot

Fine-tune or transfer-learn AlphaGenome-PyTorch on custom genomic data — pick a mode (linear probe, LoRA, Locon, full), train on BigWig tracks with agt finetune, use adapters, delta checkpoints…

genomicsxai/alphagenome-pytorch

Queries the UniProt REST API directly to search proteins, fetch FASTA sequences, map IDs between databases and read Swiss-Prot and TrEMBL entries.

davila7/claude-code-templates

Run AlphaGenome-PyTorch to get genomic track predictions — via the agt predict CLI (single locus, BED regions, whole chromosomes, raw FASTA sequences, or per-gene count tables/AnnData), variant…

genomicsxai/alphagenome-pytorch

End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.

QING1105/ezST

Guides use of deepTools on sequencing data: BAM to bigWig conversion, QC, sample correlation, and heatmaps or profiles around TSS and peaks for ChIP-seq, RNA-seq and ATAC-seq.

davila7/claude-code-templates

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

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

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

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

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

davila7/claude-code-templates

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

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

davila7/claude-code-templates

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

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

davila7/claude-code-templates

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

TianGzlab/OmicsClaw

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

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam.

GPTomics/bioSkills

Sort alignment files by coordinate or read name using samtools and pysam.

GPTomics/bioSkills

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP.

K-Dense-AI/scientific-agent-skills

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage…

K-Dense-AI/scientific-agent-skills

Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.

GPTomics/bioSkills

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…

K-Dense-AI/scientific-agent-skills

gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.

affaan-m/ECC

Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem.

K-Dense-AI/scientific-agent-skills

Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.

K-Dense-AI/scientific-agent-skills

Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Supports Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and…

K-Dense-AI/scientific-agent-skills

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference.

K-Dense-AI/scientific-agent-skills

Processes mass spectrometry data with pyOpenMS. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Stores and retrieves genomic variant calls with TileDB-VCF. An agent skill from K-Dense-AI/scientific-agent-skills.

K-Dense-AI/scientific-agent-skills

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez).

K-Dense-AI/scientific-agent-skills

Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.

K-Dense-AI/scientific-agent-skills

A skill your agent uses when querying biomedical databases (UniProt, ClinVar, gnomAD, PDB, Reactome, Open Targets, etc.) via the Biomni AgentCore Gateway MCP server.

aws-samples/amazon-bedrock-agents-healthcare-lifesciences

Computational molecular biology library (sequence I/O, alignment, phylogenetics).

lamm-mit/scienceclaw

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).

ClawBio/ClawBio

A skill your agent uses when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels…

xuzhougeng/wisp-science

Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination…

jaechang-hits/SciAgent-Skills

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results.

aipoch/medical-research-skills

Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer.

GPTomics/bioSkills