Skills real projects publish on GitHub, most starred first. Each one says what it will make an agent do before you copy it.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-amplicon-microbiome/SKILL.md
Kick off public 16S, 18S, ITS, COI, or other marker-gene amplicon microbiome workflows using nf-core/ampliseq, QIIME2, DADA2, and Cutadapt.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-analysis-router/SKILL.md
Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-atacseq-peaks-qc/SKILL.md
Run or plan ATAC-seq QC, alignment, TSS enrichment, fragment-size, blacklist, peak-calling, consensus peak, and differential accessibility workflows.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-bcl-to-fastq/SKILL.md
Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-bulk-rnaseq-counts-qc/SKILL.md
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-bulk-rnaseq-differential-expression/SKILL.md
Run or plan bulk RNA-seq differential-expression analysis from count matrices with replicate, design formula, contrast, batch, normalization, QC plot, and result-table checks.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-bulk-rnaseq/SKILL.md
Dispatch bulk RNA-seq requests to FASTQ-to-count QC or count-matrix differential-expression skills using nf-core/rnaseq, STAR, Salmon, featureCounts, MultiQC, and R/Bioconductor workflows.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-chip-cutrun-peaks-qc/SKILL.md
Run or plan ChIP-seq, CUT&RUN, or CUT&Tag QC, control handling, spike-in, peak calling, broad-vs-narrow target selection, replicate, bigWig, and differential binding workflows.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-dna-germline-variants/SKILL.md
Run or plan deep germline WGS, WES, targeted-panel, cohort, or trio variant-calling workflows with reference-build, known-sites, QC, joint-calling, and annotation checks.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-dna-somatic-variants/SKILL.md
Run or plan tumor-normal, tumor-only, WGS, WES, or cancer-panel somatic variant workflows with pairing, contamination, panel-of-normals, purity, QC, and annotation checks.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-dna-umi-panel-variants/SKILL.md
Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-dna-variant-calling/SKILL.md
Dispatch WGS, WES, or targeted DNA variant requests to germline, somatic, or UMI-panel skills, then plan public nf-core/sarek, GATK4, DeepVariant, samtools, or bcftools workflows.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-epigenomics-peaks/SKILL.md
Dispatch ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag requests to assay-specific QC, alignment, signal-track, peak-calling, consensus, and differential peak workflows.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-fastq-qc/SKILL.md
Validate FASTQ inputs, run local FastQC/MultiQC QC, interpret QC signals, and optionally execute fastp or Cutadapt trimming branches without overwriting raw reads.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-runtime-env/SKILL.md
Check whether public NGS tools and packages already exist before downloading, installing, or running a sequencing pipeline.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-scrna-seq/SKILL.md
Route single-cell or single-nucleus RNA-seq FASTQs to public count-generation workflows and defer post-count matrix QC, annotation, clustering, and UMAP analysis to the embedded scrna-seq-qc skill.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/ngs-shotgun-metagenomics/SKILL.md
Kick off public shotgun metagenomics QC, host-depletion, taxonomic profiling, and functional profiling workflows using nf-core/taxprofiler, Kraken2, Bracken, MetaPhlAn, and HUMAnN.
OpenAISkillopenai/plugins/plugins/ngs-analysis/skills/scrna-seq-qc/SKILL.md
Process, quality-control, annotate, and visualize single-cell or single-nucleus RNA-seq datasets across tissues and species. Use when Codex needs to build, adapt, or review a general scRNA-seq QC pipeline; choose dataset-appropriate cell-level filters from QC distributions; run required scDblFinder-based doublet and ambient-RNA filtering; annotate cells with matched references or marker-based fallbacks; or generate global and per-group UMAP visualizations for large scRNA-seq datasets.
OpenAISkillopenai/plugins/plugins/notion/skills/notion-knowledge-capture/SKILL.md
Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.
OpenAISkillopenai/plugins/plugins/notion/skills/notion-meeting-intelligence/SKILL.md
Prepare meeting materials with Notion context and supplemental research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees.
A folder with a SKILL.md file: a name, a description of when to use it, and instructions. Claude loads a skill only when the task matches its description.
Copy the folder into your project's .claude/skills/ directory, or into your own skills folder to use it everywhere.
We read each file for commands that read secrets, delete things or pipe downloads into a shell, and say so before you copy it. No warning is not a promise that a file is safe.
Open a skill to see its discussion. Reports from people and their agents are coming.
