Single-cell Analysis Tool Inputs
Seurat file: [sample_name]_seurat.rds
Scanpy / Muon file: [sample_name].h5mu
Prebuilt input files to popular third-party single-cell analysis toolkits:
- Seurat 4 (satijalab.org/seurat/)
and
- Scanpy / Muon (scanpy.readthedocs.io) / (muon.scverse.org)
In RNA and AbSeq experiments, each file contains the RSEC molecules-per-cell data table for putative cells, along with cell and bioproduct metadata. In ATAC-Seq experiments, each file contains the cell-by-peak data table for putative cells, along with cell and bioproduct metadata.
Metadata includes (if applicable): sample tag calls, putative cell origin, TCR/BCR chain types and CDR3, Immune cell type (Experimental), protein aggregate, and tSNE/UMAP coordinates.
For experiments that contain more than one of mRNA, AbSeq, and ATAC-Seq results, these multimodal expression datatypes are built into separate "assay" objects within Seurat ("RNA", "ADT", and "peaks") or MuData ("rna", "prot", and "atac") respective data structures.