Scanpy
Standard single-cell RNA-seq workflow from QC through clustering and marker genes.
Install
Ships scriptsnpx skills add K-Dense-AI/scientific-agent-skills
scRNA-seq analysis: QC, normalization, UMAP/PCA, clustering, marker genes, or converting an RDS object to h5ad.
- Author
- K-Dense Inc.
- License
- BSD-3-Clause
Walks the established Scanpy path: quality control, normalization, PCA, UMAP or t-SNE, Leiden clustering, differential expression and plotting. It also handles the awkward first step of converting Seurat or SingleCellExperiment RDS files into h5ad before anything else can run. Dask is documented for datasets that do not fit in memory, and probabilistic models are pointed elsewhere.
Similar skills
PyDESeq2
SkillRuns bulk RNA-seq differential expression in Python instead of R.
AnnData
SkillThe h5ad data structure that sits under the scverse single-cell stack.
scvi-tools
SkillProbabilistic single-cell models for batch correction and integration.
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