alterlab-anndata
From the author
Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handling layers/obsm/backed-mode; for the QC, normalization, clustering, UMAP, and differential-expression analysis pipeline prefer alterlab-scanpy instead, and for RNA velocity from spliced/unspliced layers prefer alterlab-scvelo instead. Part of the AlterLab Academic Skills suite.
Install
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-anndata -a claude-code
Installs to .claude/skills/alterlab-anndata/ · Each command fetches the skill straight from GitHub with the open skills CLI.
Byte-identical to the scanned commit, with the repository’s licence and a SOURCE.txt.
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- anndataK-Dense-AI/scientific-agent-skillsHandles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.Other★ 54.4K
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- alterlab-scientific-writingAlterLab-IEU/AlterLab-Academic-SkillsWrites scientific manuscripts in full flowing paragraphs (never bullet points) via a two-stage process — section outlines with key points using alterlab-research-lookup, then conversion to prose — applying IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and current reporting guidelines (CONSORT 2025, STROBE, PRISMA 2020, TRIPOD+AI). Use when drafting or revising a research paper section by section (abstract, introduction, methods, results, discussion), tightening scientific prose, or writing professional/technical reports. For the end-to-end multi-agent paper pipeline (APA 7 LaTeX/DOCX output, bilingual abstracts, reviewer-driven revision roadmap) use alterlab-paper-writer; for a specific venue's LaTeX template and house style use alterlab-venue-templates; to build a BibTeX bibliography use alterlab-citation-mgmt. Part of the AlterLab Academic Skills suite.Science★ 78
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