alterlab-anndata
De la autor
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.
Instalare
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-anndata -a claude-code
Se instalează în .claude/skills/alterlab-anndata/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
Identic octet cu octet cu commit-ul scanat, cu licența depozitului și un fișier SOURCE.txt.
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Verificări de siguranță pe SKILL.md
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De ce 83
aiqbench calculează scorul de încredere din semnale publice. Nu este un audit de securitate, așa că citește un skill înainte să-l instalezi.
Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- anndata-data-structurejaechang-hits/SciAgent-SkillsAnnotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.Știință★ 382
- 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.Altele★ 54.4K
- alterlab-scgptAlterLab-IEU/AlterLab-Academic-SkillsApply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.Știință★ 78
- alterlab-daskAlterLab-IEU/AlterLab-Academic-SkillsScales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed task graphs, and cluster execution. Use when existing pandas/NumPy code must run on larger-than-RAM data or across clusters, for parallel file processing, distributed ML, or integration with existing pandas code. For out-of-core analytics on a single machine prefer vaex; for in-memory speed prefer polars. Part of the AlterLab Academic Skills suite.Date★ 78
- 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.Știință★ 78
- alterlab-cellxgeneAlterLab-IEU/AlterLab-Academic-SkillsQuery the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.Altele★ 78
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