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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Run AlphaGenome-PyTorch to get genomic track predictions — via the agt predict CLI (single locus, BED regions, whole chromosomes, raw FASTA sequences, or per-gene count tables/AnnData), variant… | genomicsxai/ | 162 | — | ~868 | Automated safety check: Pass | Apache-2.0 | 26 days ago |
| 2 | Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots. | davila7/ | 33k | 11 repos | ~4k | Automated safety check: Pass | MIT | today |
| 3 | 3.Lamindb Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation, query/search, collections, branches, storage… | K-Dense-AI/ | 48k | 1 repo | ~2.1k | Automated safety check: Pass | Apache-2.0 | 6 days ago |
| 4 | Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis. | ClawBio/ | 1.2k | 1 repo | ~2k | Automated safety check: Pass | MIT | 2 days ago |
| 5 | 5.Pydeseq Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for… | aipoch/ | 1.9k | — | ~1.8k | Automated safety check: Pass | MIT | 24 days ago |
| 6 | Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files. | FreedomIntelligence/ | 3.1k | 1 repo | ~850 | Automated safety check: Pass | No licence | 2 mo ago |
| 7 | Load when building the neighbour graph, embedding (UMAP/t-SNE/diffmap/PHATE), and clustering (Leiden/Louvain) on a normalised single-cell AnnData. | TianGzlab/ | 161 | — | ~2.4k | Automated safety check: Pass | Apache-2.0 | 4 days ago |
| 8 | 8.Sc Grn Load when inferring TF → target gene regulatory networks on a normalised scRNA AnnData via pySCENIC (GRNBoost2 + cisTarget + AUCell) or correlation-based GRN fallback (when arboreto is unavailable… | TianGzlab/ | 161 | — | ~1.7k | Automated safety check: Pass | Apache-2.0 | 4 days ago |
| 9 | Load when inferring copy-number variation per spot on a preprocessed spatial AnnData with chromosome-annotated genes via infercnvpy (default — log-ratio sliding-window) or Numbat (R, allele-aware… | TianGzlab/ | 161 | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | 4 days ago |
| 10 | Load when ranking spatially variable genes with Moran's I, SpatialDE, SPARK-X, or FlashS. | TianGzlab/ | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | 4 days ago |
| 11 | Load when running spatial autocorrelation / hotspot / co-occurrence / neighbourhood-enrichment / Ripley K stats on a clustered spatial AnnData via squidpy. | TianGzlab/ | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | 4 days ago |
