Format
Loom
HDF5-based matrix format from the Linnarsson lab; produced by velocyto for spliced and unspliced layers.
Extensions: .loom · Coordinates: n/a · Specification
From Loom
- How to Convert Loom to Seurat object (Without Losing Your Metadata)
SeuratDisk's Connect-then-as.Seurat path works, but velocyto barcodes and Seurat v5 layers will quietly wreck your merge if you skip the cleanup step.
To Loom
- How to Convert Seurat object to Loom (Without Losing Your Metadata)
SaveLoom writes one assay and can quietly hand you scaled data instead of raw counts, so check the matrix before you trust it in pySCENIC or velocyto.