2,000+ deep skill bundles for AI bioinformatics agents

Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol

Use when working with CVXPY — a Python-embedded domain-specific language for convex optimization problems. Covers problem construction with the DCP (Disciplined Convex Programming) ruleset, all built-

wateRmelon v2.16.0 — Bioconductor R package for Illumina 450K and EPIC DNA methylation array normalization and performance metrics. Provides 15 normalization methods (dasen, nasen, naten, danes, swan,

Use when working with aurora — a machine learning GWAS R package for identifying microbial habitat adaptation genes and autochthonous strain provenance. Implements a Random Forest + random-walk (AUtoc

SeSAMe (SEnsible Step-wise Analysis of DNA MEthylation BeadChips) — R/Bioconductor package for processing Illumina Infinium DNA methylation arrays. Supports EPIC, EPICv2, HM450, HM27, MM285, and Mamma

JM / JMbayes2 — Joint models for longitudinal and time-to-event data under the Bayesian framework. Fits shared-parameter joint models via jm() linking mixed-effects longitudinal submodels (lme, mixed_

Stan — probabilistic programming language for Bayesian statistical modeling and high-performance inference. Full Bayesian inference via No-U-Turn Sampler (NUTS/HMC), approximate inference via Automati

PubMed Database — NCBI's comprehensive biomedical literature database providing free access to over 37 million citations from MEDLINE, life science journals, and online books. Query via E-utilities RE

PyStan — Python interface to Stan for Bayesian statistical modeling and high-performance inference. Compile Stan programs (stan.build), draw posterior samples via HMC-NUTS (model.sample), extract draw

ClinVar Database — NCBI's public archive of human genetic variant clinical significance. Query via E-utilities REST API (esearch, esummary, efetch, elink) or download bulk data from FTP in XML, VCF, a

Deep learning system for protein structure prediction from amino acid sequence with atomic accuracy — revolutionized structural biology.

cmprsk — Subdistribution Analysis of Competing Risks. R package providing non-parametric cumulative incidence estimation via cuminc() with Gray's K-sample test for group comparisons, Fine & Gray propo

Spectral Python (SPy) routing skill for hyperspectral image data representation, manipulation, and processing. Use this skill when users mention SPy, spectralpython, hyperspectral imagery, ENVI header

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

nc-time-axis provides cftime-aware axis support for matplotlib, enabling the plotting of time series that use non-standard calendars (360_day, noleap, all_leap, julian, etc.) common in climate, weathe

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