In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Filter cells based on QC metrics and MAD threshold (r cfg$MAD_THRESHOLD):

• Low number of UMI (lower tail).
• Low number of detected genes (lower tail).
• High expression of mitochondrial genes (upper tail).

r get_used_qc_filters_operator_desc(cfg$CUSTOM_FILTERS_OPERATOR)

Removing r sum(qc_filter) low quality cells based on MAD.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.