Generate Expression Matrix Datatables
RSEC-adjusted molecule counts and DBEC-adjusted molecule counts for each putative cell are presented in matrix market exchange format (MEX). RSEC molecule counts per cell are also preloaded, along with cell metadata, into popular analysis package formats:
- Seurat (.rds)
- Scanpy / Muon (.h5mu)
In addition, an unfiltered expression matrix is output in matrix market exchange format (MEX) for all cell labels that had at least 10 reads associated with them.
During this step, two dimensionality reduction methods are run on the expression data to generate tSNE and UMAP coordinates of the putative cells.