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AI & LLM Engineering · AnnData
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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 | 2.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 |
| 3 | 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 |
| 4 | 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 | 3 days ago |
| 5 | Load when aggregating single cells into metacells (sample-aware coarse-grained pseudo-cells) on a normalised scRNA AnnData via SEACells or KMeans on a low-D embedding. | TianGzlab/ | 161 | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | 3 days ago |
| 6 | Load when removing batch effects from multi-batch spatial AnnData with PCA using Harmony, BBKNN, or Scanorama. | TianGzlab/ | 161 | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | 3 days ago |
