EmptydropsR is a statistical method that distinguishes between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment. It identifies real cells by detecting significant deviations from the expression profile of the ambient solution.
This version of the workflow is designed to take 10X's raw feature matrix.mtx as input. In other words, the input is a .mtx file of genes (rows) x cells (cols).
This workflow outputs two files:
metadata.h5:stores values of arguments (inputs to emptydropsR) during run time.output.h5:returns aLogProb,PValue, andFDRthat should be used by the user to filter out emptydrops.
More information can be found here: https://rdrr.io/github/MarioniLab/DropletUtils/man/emptyDrops.html
The manuscript can be found here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1662-y
The source code can be found here: https://github.com/MarioniLab/DropletUtils