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| # | 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/ | 228 | 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/ | 33k | 12 repos | ~3.6k | Automated safety check: Pass | MIT | yesterday |
| 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/ | 33k | 11 repos | ~1.8k | Automated safety check: Pass | MIT | yesterday |
| 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 | 5 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 | 5 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 | 5 days ago |
| 7 | 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/ | 228 | 4 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | 3 mo ago |
| 8 | 8.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 | 5 days ago |
| 9 | Annotated matrices for single-cell genomics. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 374 | 2 repos | ~5.8k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
| 10 | 10.Scvelo RNA velocity analysis with scVelo. An agent skill from lamm-mit/scienceclaw. | lamm-mit/ | 246 | 4 repos | ~524 | Automated safety check: Pass | BSD-3-Clause | 1 mo ago |
| 11 | 11.Scanpy Standard single-cell RNA-seq analysis pipeline. An agent skill from aipoch/medical-research-skills. | aipoch/ | 1.9k | — | ~3.9k | Automated safety check: Pass | MIT | 23 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/ | 1.9k | — | ~1.5k | Automated safety check: Pass | MIT | 23 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/ | 374 | 2 repos | ~7.2k | Automated safety check: Pass | BSD-3-Clause | 12 days ago |
