Library
scvi-tools agent skills for Claude Code, Codex and other agents.
- skills
- 14
- Type
- Library
- Website
- scvi-tools.org
- Official GitHub
- scverse
scvi-tools skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | 1.Scgpt Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. | JimLiu/ | 227 | 4 repos | ~1.3k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 2 | Manages biological datasets with LaminDB: versioned artifacts, run lineage, ontology-based annotation, schema validation and links to workflow managers and ML tools. | davila7/ | 32k | 12 repos | ~3.6k | Automated safety check: Pass | MIT | today |
| 3 | This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. | davila7/ | 32k | 12 repos | ~1.8k | Automated safety check: Pass | MIT | today |
| 4 | 4.Scanpy Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or… | K-Dense-AI/ | 48k | 1 repo | ~5.1k | Automated safety check: Pass | BSD-3-Clause | 2 days ago |
| 5 | Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Notes | MIT | 2 days ago |
| 6 | Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. | K-Dense-AI/ | 48k | 1 repo | ~2.6k | Automated safety check: Pass | BSD-3-Clause | 2 days ago |
| 7 | Annotated matrices for single-cell genomics. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 370 | 2 repos | ~5.8k | Automated safety check: Pass | BSD-3-Clause | 8 days ago |
| 8 | Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. | JimLiu/ | 227 | 4 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 9 | 9.Anndata Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem. | K-Dense-AI/ | 48k | 1 repo | ~3.9k | Automated safety check: Notes | BSD-3-Clause | 2 days ago |
| 10 | 10.Scvelo RNA velocity analysis with scVelo. An agent skill from majiayu000/claude-skill-registry. | majiayu000/ | 666 | 5 repos | ~2.6k | Automated safety check: Pass | BSD-3-Clause | today |
| 11 | 11.Scanpy Standard single-cell RNA-seq analysis pipeline. An agent skill from aipoch/medical-research-skills. | aipoch/ | 2k | — | ~3.9k | Automated safety check: Pass | MIT | 20 days ago |
| 12 | 12.Scvi Tools Deep generative models for single-cell omics; use when you need probabilistic batch correction (scVI), transfer learning, uncertainty-aware differential expression, or multimodal integration… | aipoch/ | 2k | — | ~1.5k | Automated safety check: Pass | MIT | 20 days ago |
| 13 | Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with… | jaechang-hits/ | 370 | 2 repos | ~7.2k | Automated safety check: Pass | BSD-3-Clause | 8 days ago |
| 14 | Load when deconvolving spot-level cell-type proportions on a Visium-style spatial AnnData using a labelled scRNA reference (FlashDeconv / Cell2location / RCTD / DestVI / Tangram / others). | TianGzlab/ | 161 | — | ~1.9k | Automated safety check: Pass | MIT | 2 mo ago |
Questions, answered from the data.
What is the best scvi-tools skill?
Scgpt from JimLiu/science-skills ranks first of the 14 scvi-tools skills listed here, with the highest score: its repository has 227 GitHub stars, 4 other GitHub owners carry a copy, its SKILL.md loads about 1.3k tokens and it passes the automated safety check with no findings. Next come LaminDB Biological Data Management and Scvi Tools.
Is there an official scvi-tools skill?
None yet. All 14 scvi-tools skills listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.