This simple R package can be used to calculate a useful QC metric for single cell RNA-seq datasets generated with the 10x Genomics Chromium Single Cell Gene Expression platform: the nuclear fraction score. This score captures, for each input cell barcode, the fraction of RNA that likely originated from unspliced (nuclear) pre-mRNA. Sheared cell membranes from damaged cells in the input cell suspension primarily release cytoplasmic RNA into solution, while the nuclear envelope remains intact. As a result, RNA released from stressed or damaged cells consists mostly of mature cytoplasmic mRNA and is relatively depleted of unspliced nuclear precursor mRNA. This fact can be useful in identifying both; droplets containing only ambient RNA, characterised by a low nuclear fraction score, and damaged cells, which can be identified by a high score. The QC metric is calculated by parsing the input barcoded BAM file for CB and RE flags added by 10x Genomics' Cell Ranger software.
