An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
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Updated
Mar 11, 2026 - R
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
.h5mu files interface for Seurat
MuData-compatible storage for bioconductor's MultiAssayExperiment
Seurat v5 compatible HDF5 converter for single-cell data — h5ad, h5Seurat, h5mu, Loom with full spatial data support
Pipeline to download the HCA Human Tonsil Atlas, extract raw counts and cell-type annotations from the HCATonsilData Bioconductor package, and export a compressed .h5ad file ready for python sc-verse analysis such as scVI model training. Reproducible environment managed with Pixi (R + Python).
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