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BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes
| Date | Stars |
|---|---|
| 2026-07-31 | 755 |
| 2026-08-03 | 776 |
| 2026-08-06 | 776 |
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# BioMate-KB — Bioconductor Skills **200 Bioconductor packages — the top 100 most-downloaded plus the top 100 rising stars — formatted as Claude Code Skills.** A skill bundle in [Claude Code Skills](https://docs.anthropic.com/en/docs/claude-code/skills-overview) format. It covers the 100 most-used Bioconductor packages **and** the top 100 rising-star packages (newly released since ~2021 and fast-growing) from the BioMate-KB knowledge base. Each skill teaches Claude when to choose a package, **the workflows it supports** (each analysis as a recipe), what parameters to set, how to interpret results, and what pitfalls to avoid. ## What's here ``` skills/ (200 packages · 12 domains) ⭐ = rising star ├── transcriptomics/ (97 — DESeq2, edgeR, limma · ⭐ standR, Voyager, sechm, crisprScore) ├── genomics/ (33 — GenomicRanges, Biostrings · ⭐ rBLAST, syntenet, ggmanh) ├── general/ (19 — Biobase, DOSE · ⭐ immunotation, faers, mosbi) ├── proteomics/ (16 — MSnbase, mixOmics, mzR · ⭐ MatrixQCvis, MsDataHub, TargetDecoy) ├── epigenomics/ (10 — ChIPseeker, minfi · ⭐ HiCExperiment, HiContacts, epigraHMM) ├── single-cell/ (8 — SingleCellExperiment · ⭐ demuxmix, hoodscanR, MuData) ├── variant-calling/ (4 — VariantAnnotation, snpStats, vsn) ├── metagenomics/ (4 — phyloseq, microbiome, DirichletMultinomial) ├── imaging/ (4 — flowCore, EBImage · ⭐ lisaClust, cytoviewer) ├── annotation/ (2 — biomaRt, KEGGgraph) ├── enrichment/ (2 — enrichplot, ReactomePA) └── metabolomics/ (1 — ⭐ rgoslin) ``` A package that supports multiple analyses lists each as a `### ` recipe under a **`## Workflows`** section (e.g. DESeq2 → standard / multi-factor / LRT; crisprscore → on-target / off-target / indel scoring). The most-used 100 cover ~56% of Bioconductor analysis-package download volume; the rising-star 100 surface newly-important methods before they reach the top by volume. Beyond this 200-package sample, the full BioMate KB has runnable workflows for **1,818** Bioconductor packages — **~87% of analysis-package download volume** — available via [BioMate Cloud](https://biomate.ai). **Bioconductor version:** these skills are grounded against **Bioconductor 3.21** (pinned explicitly — `release` is a moving pointer that drops packages as it advances, e.g. several rising stars dropped out of 3.23). The pinned version is recorded in `MANIFEST.json` (`bioconductor_version`); re-fetch a different snapshot with `BIOC_VERSION=… python3 extraction/fetch_authoritative_sources.py`. ## Full package list All **200 packages** — with category, description, and the workflows each one supports — are in **[PACKAGES.md](PACKAGES.md)** (one page, four columns; ⭐ marks rising stars). ### Packages per domain  ### Workflows per domain A package with multiple analyses contributes one `### ` recipe subsection per workflow — **390 workflows across the 200 packages; 89 are multi-workflow** (e.g. DESeq2 → DE / multi-factor / QC-transform / LRT; crisprScore → 6 scoring recipes).  ## How these 200 were selected Two ranked sets of 100: - **Top 100 by downloads** — ranked purely by the official Bioconductor download score (`bioc_pkg_scores.tab`). These cover **~56% of Bioconductor analysis-package download volume**. Because the rank is by raw volume, this set includes both **analysis tools** (DESeq2, edgeR, limma, fgsea, …) and the **foundational data-structure / I/O / annotation** packages nearly every analysis imports (GenomicRanges, Biostrings, SingleCellExperiment, AnnotationHub, …). - **Top 100 rising stars** — restricted to **analysis** packages (infrastructure, data-container, and GUI packages excluded), recently released (first release ≥ 2021) and fast-growing in 2025 (year-over-year download growth + ≥ 3,000 distinct download IPs), ranked by 2025 downl
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Would you bet a product on this? Bounded 0–100 and slow moving.
matched fp:55d49c18d7f79473, llm:Repository description: 'BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes'
matched fp:55d49c18d7f79473, llm:Repository description: 'BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes'
matched fp:55d49c18d7f79473, llm:Repository description: 'BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes'