2,000+ deep skill bundles for AI bioinformatics agents

DBSCAN (Density-Based Spatial Clustering of Applications with Noise) — fast C++ implementation of density-based clustering algorithms in R. Includes DBSCAN, HDBSCAN, OPTICS/OPTICSXi, LOF outlier detec

Zarr — chunked, compressed N-dimensional arrays for Python with cloud-native storage. Provides hierarchical groups, pluggable compression codecs (Blosc, Zstd, Gzip), sharding for large-scale datasets,

Reactome — curated pathway knowledgebase and analysis platform for pathway enrichment, expression overlay, and species comparison. Use when user needs pathway over-representation analysis (ORA) with R

xESMF — Regrid geospatial and climate datasets between structured grids using ESMF (Earth System Modeling Framework). Use when working with climate model output (CMIP6, ERA5, CESM), satellite data, or

Query STRING API for protein-protein interaction networks, functional enrichment, and interaction partner discovery. Covers 59M proteins across 5000+ species with 20B+ scored interactions from 7 evide

TCGAbiolinks for searching, downloading, and analyzing cancer genomics data from the NCI Genomic Data Commons (GDC). Routes tasks for GDCquery/GDCdownload, data preparation with GDCprepare, differenti

Uni-Mol universal 3D molecular representation learning framework for molecular property prediction, protein-ligand docking, drug-target interaction, and binding affinity scoring. Covers unimol_tools P

Direct REST API access to UniProt (250M+ protein sequences, 570K+ reviewed Swiss-Prot entries). Protein search, FASTA/JSON retrieval, ID mapping across 200+ databases, batch retrieval, streaming, fiel

Programmatic access to the U.S. EPA ToxCast and Tox21 high-throughput screening (HTS) bioactivity data via the CTX APIs. Use to query chemical hazard profiles, AC50 values, and hit-calls across thousa

Ensembl VEP (Variant Effect Predictor) — annotates genomic variants with gene, transcript, protein, and regulatory consequences using Ensembl's annotation framework. Supports VCF, HGVS, and genomic co

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

t-SNE (t-distributed Stochastic Neighbor Embedding) for nonlinear dimensionality reduction and visualization of high-dimensional data. Covers Barnes-Hut and exact modes, FIt-SNE/openTSNE interpolation

xorca (eXtensible ORCA Grid Adapter) preprocesses NEMO ocean model NetCDF outputs into XGCM-compatible Xarray datasets for grid-aware operations on curvilinear ORCA grids. Use when working with NEMO s

ChAMP — Chip Analysis Methylation Pipeline for Illumina 450K and EPIC arrays. Integrated R/Bioconductor pipeline for DNA methylation analysis covering IDAT loading, quality control, normalization (BMI

GEO Database — NCBI Gene Expression Omnibus public repository for high-throughput gene expression and functional genomics data. Contains 264,000+ series (GSE), 8M+ samples (GSM), 27,000+ platforms (GP

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

BEDTools — Swiss-army knife for genome arithmetic on genomic intervals. Provides intersect, merge, subtract, complement, closest, window, coverage, genomecov, slop, flank, sort, groupby, getfasta, mas

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

fdrtool — estimation of tail area-based false discovery rates (Fdr/q-values) and density-based local false discovery rates (fdr) from observed test statistics. Supports four null models: normal (z-sco