Bioinformatics

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

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.

bioMate-AI/biomate-bioconductor-kb

Activate this skill for "/genomi decode", "decode my genome", "decode my DNA", "show me the dashboard", "the Genomi dashboard", "one-shot rundown", or any all-at-once request that asks Genomi to…

exon-research/genomi

Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL.

GPTomics/bioSkills

Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways

ClawBio/ClawBio

Fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames…

ClawBio/ClawBio

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

K-Dense-AI/scientific-agent-skills

Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data.

K-Dense-AI/scientific-agent-skills

Builds and operates reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow.

K-Dense-AI/scientific-agent-skills

Analyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4.

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

Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog.

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

Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data.

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

Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression.

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

Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.

QING1105/ezST

Omics and single-cell workflow guide for AnnData, Scanpy-style dataset profiling, PyDESeq2-oriented count checks, pysam alignment inspection, and pyOpenMS mass-spectrometry summaries.

DrugClaw/DrugClaw

Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.

TianGzlab/OmicsClaw

A skill your agent uses when a developer asks how to get started building healthcare or life sciences agents, wants to understand the HCLS Agents Toolkit, or asks what's available in this repository.

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

Gateway to 400+ bioinformatics skills from bioSkills and ClawBio.

Tommy-yw/RunbookHermes

Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.

bioMate-AI/biomate-bioconductor-kb

Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.

ClawBio/ClawBio

Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights.

K-Dense-AI/scientific-agent-skills

Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression.

JimLiu/science-skills

ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds.

GPTomics/bioSkills

Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture

ClawBio/ClawBio

Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions

ClawBio/ClawBio

Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.

ClawBio/ClawBio

Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.

ClawBio/ClawBio

Classic Visium platform branch of the spatial transcriptomics workflow — spot-level 5-stage pipeline (load+QC, normalize+cluster, domains+SVG, deconvolution, downstream prep).

QING1105/ezST

Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.

TianGzlab/OmicsClaw

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

Generates transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M.

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

Annotated matrices for single-cell genomics. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.

bioMate-AI/biomate-bioconductor-kb

Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+.

GPTomics/bioSkills

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

lamm-mit/scienceclaw

Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice.

NVIDIA/skills

Xenium platform branch of the spatial transcriptomics workflow — load and validate the platform's cell-level matrix for downstream analysis.

QING1105/ezST

Load when querying STRING for the protein-protein interaction neighborhood of a bulk RNA-seq DEG list and finding hub genes.

TianGzlab/OmicsClaw

Build/run/audit bulk RNA, sc/snRNA and spatial workflows with traceable QC; not mechanism claims.

huang-sir1/radiology-skills