Comments
Code comments and annotations
iterate-pr
by getsentry
Iterate on a PR until CI passes. Use when you need to fix CI failures, address review feedback, or continuously push fixes until all checks are green. Automates the feedback-fix-push-wait cycle.
single-cell-annotation-skills-with-omicverse
by Starlitnightly
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
tcga-bulk-data-preprocessing-with-omicverse
by Starlitnightly
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
Universal Single-Cell Annotator
by majiayu000
The most comprehensive Claude Code skills registry Web Search: https://skills-registry-web.vercel.app
skill-installer
by aiskillstore
Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos).
latex-document
by ndpvt-web
Universal LaTeX document skill: create, compile, and convert any document to professional PDF with PNG previews. Supports resumes, reports, cover letters, invoices, academic papers, theses/dissertations, academic CVs, presentations (Beamer), scientific posters, formal letters, exams/quizzes, books, cheat sheets, reference cards, exam formula sheets, fillable PDF forms (hyperref form fields), conditional content (etoolbox toggles), mail merge from CSV/JSON (Jinja2 templates), version diffing (latexdiff), charts (pgfplots + matplotlib), tables (booktabs + CSV import), images (TikZ), Mermaid diagrams, AI-generated images, watermarks, landscape pages, bibliography/citations (BibTeX/biblatex), multi-language/CJK (auto XeLaTeX), algorithms/pseudocode, colored boxes (tcolorbox), SI units (siunitx), Pandoc format conversion (Markdown/DOCX/HTML ↔ LaTeX), and PDF-to-LaTeX conversion of handwritten or printed documents (math, business, legal, general). Compile script supports pdflatex, xelatex, lualatex with auto-detection, latexmk backend, texfot log filtering, PDF/A output, and verbosity control (--verbose/--quiet). Empirically optimized scaling: single agent 1-10 pages, split 11-20, batch-7 pipeline 21+. Use when user asks to: (1) create a resume/CV/cover letter, (2) write a LaTeX document, (3) create PDF with tables/charts/images, (4) compile a .tex file, (5) make a report/invoice/presentation, (6) anything involving LaTeX or pdflatex, (7) convert/OCR a PDF to LaTeX, (8) convert handwritten notes, (9) create charts/graphs/diagrams, (10) create slides, (11) write a thesis or dissertation, (12) create an academic CV, (13) create a poster, (14) create an exam/quiz, (15) create a book, (16) convert between document formats (Markdown, DOCX, HTML to/from LaTeX), (17) generate Mermaid diagrams for LaTeX, (18) create a formal business letter, (19) create a cheat sheet or reference card, (20) create an exam formula sheet or crib sheet, (21) condense lecture notes/PDFs into a cheat sheet, (22) create a fillable PDF form with text fields/checkboxes/dropdowns, (23) create a document with conditional content/toggles (show/hide sections), (24) generate batch/mail-merge documents from CSV/JSON data, (25) create a version diff PDF (latexdiff) highlighting changes between documents, (26) create a homework or assignment submission with problems and solutions, (27) create a lab report with data tables, graphs, and error analysis, (28) encrypt or password-protect a PDF, (29) merge multiple PDFs into one, (30) optimize/compress a PDF for web or email, (31) lint or check a LaTeX document for common issues, (32) count words in a LaTeX document, (33) analyze document statistics (figures, tables, citations), (34) fetch BibTeX from a DOI, (35) convert a Graphviz .dot file to PDF/PNG, (36) convert a PlantUML .puml file to PDF/PNG, (37) create a one-pager/fact sheet/executive summary, (38) create a datasheet or product specification sheet, (39) extract pages from a PDF (page ranges, odd/even), (40) check LaTeX package availability before compiling, (41) analyze citations and cross-reference with .bib files, (42) debug LaTeX compilation errors, (43) make a document accessible (PDF/A, tagged PDF), (44) create lecture notes or course handouts, (45) fill an existing PDF form (fillable fields or non-fillable with annotations), (46) extract text or tables from a PDF (pdfplumber, pypdf), (47) OCR a scanned PDF to text (pytesseract), (48) create a PDF programmatically with reportlab (Canvas, Platypus), (49) rotate or crop PDF pages (pypdf), (50) add a watermark to an existing PDF, (51) extract metadata from a PDF (title, author, subject).
single-cell-cellphonedb-communication-mapping
by Starlitnightly
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
code-walk-thru
by pchalasani
Use this when user wants you to walk through (code or text) files in a EDITOR to either explain how some code works, or to show the user what changes you made, etc. You would typically use this repeatedly to show the user your changes or code files one by one, sometimes with specific line-numbers. This way the user is easily able to follow along in their favorite EDITOR as you point at various files possibly at specific line numbers within those files.
tooluniverse-epigenomics
by mims-harvard
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse annotation tools (Ensembl, ENCODE, SCREEN, JASPAR, ReMap, RegulomeDB, ChIPAtlas). Supports BED, BigWig, methylation beta-value matrices, Illumina manifest files, and multi-sample clinical data. Use when processing methylation data, ChIP-seq peaks, ATAC-seq signals, or answering questions about CpG sites, differential methylation, chromatin accessibility, histone marks, or epigenomic statistics.
tooluniverse-phylogenetics
by mims-harvard
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval (NCBI, UniProt, Ensembl) and tree annotation. Use when processing FASTA/PHYLIP/Nexus/Newick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.
tooluniverse-gwas-snp-interpretation
by mims-harvard
Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open Targets Genetics, ClinVar). Retrieves variant annotations, GWAS trait associations, fine-mapping evidence, locus-to-gene predictions, and clinical significance. Use when asked to interpret a SNP by rsID, find disease associations for a variant, assess clinical significance, or answer questions like "What diseases is rs429358 associated with?" or "Interpret rs7903146".
tooluniverse-gene-enrichment
by mims-harvard
Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis, GO term enrichment, KEGG pathway analysis, GSEA, over-representation analysis, functional annotation, or gene set analysis.
testing-hashql
by hashintel
HashQL testing strategies including compiletest (UI tests), unit tests, and snapshot tests. Use when writing tests for HashQL code, using //~ annotations, running --bless, debugging test failures, or choosing the right testing approach.
skill-installer
by ComposioHQ
Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos).
issue-triage
by ComposioHQ
Triage Linear or Jira backlogs and run bug sweeps via the Composio CLI. Bulk-fetch issues, dedupe, relabel, reassign, and post summaries — all from the shell without clicking through the UI.
update-docs
by meta-pytorch
Update documentation across the repo after API changes. Finds stale references in docs, examples, docstrings, and fixes them.
pr-review-ci-fix
by ComposioHQ
Automated PR review and CI auto-fix for GitHub and GitLab using the Composio CLI. Pulls diffs, fetches failing job logs, posts review comments, and loops fix commits until checks go green.
Design Rationale
by product-on-purpose
A curated collection of 24 best-practice, plug-and-play product management “agent skills” plus templates and workflow bundles for consistent, professional PM outputs.
ascii-mini-charts
by partme-ai
Generate ASCII mini charts (sparkline/bar/simple line) for plain-text trend inspection, with minimal + annotated variants and normalization notes.
xhs-content-ops
by autoclaw-cc
小红书复合内容运营技能。组合搜索、详情、发布、互动等能力完成运营工作流。 当用户要求竞品分析、热点追踪、内容创作、互动管理等复合任务时触发。
agentation-self-driving
by benjitaylor
Autonomous design critique mode using the Agentation annotation toolbar. Use when the user asks to "critique this page," "add design annotations," "review the UI," "self-driving mode," "auto-annotate," or wants an AI agent to autonomously add design feedback annotations to a web page via the browser. Requires the Agentation toolbar to be installed on the target page and agent-browser skill to be available.
release-publish
by mono
Publish SkiaSharp packages and finalize the release. Use when user says "publish X", "finalize X", "tag X", or "finish release X". This is the FINAL step - after release-testing passes. Publishes to NuGet.org, creates tag, GitHub release, and closes milestone. Triggers: "publish the release", "push to nuget", "create github release", "tag the release", "close the milestone", "annotate release notes", "testing passed what's next", "finalize 3.119.2", "release is ready".
bcftools-variant-manipulation
by jaechang-hits
"Command-line toolkit for VCF/BCF variant file manipulation. Filter, merge, annotate, query, normalize, and compute statistics on variant call files. Essential for post-variant-calling pipelines: quality filtering, multi-sample merging, rsID annotation, and genotype extraction. Companion to samtools in the HTSlib ecosystem. Use GATK instead for complex indel realignment during variant calling; use VCFtools instead for population genetics statistics."
documentation-templates
by vudovn
Documentation templates and structure guidelines. README, API docs, code comments, and AI-friendly documentation.