Analysis#

qc

Subsets each cell type to samples passing quality control (QC).

library_size

Calculate normalization factor-adjusted library sizes for each sample in each cell type, via the approach of edgeR's calcNormFactors().

cpm

Calculate counts per million for each cell type.

log_cpm

Calculate log counts per million for each cell type.

regress_out

Regress out covariates from obs.

de

Perform differential expression (DE) on a Pseudobulk dataset with limma-voom.