scruff (Single Cell RNA-Seq UMI Filtering Facilitator) is a package for processing single cell RNA-seq (scRNA-seq) FASTQ reads generated by CEL-Seq and CEL-Seq2 protocols. It demultiplexes scRNA-seq FASTQ files, aligns reads to reference genome using Rsubread, and generates UMI filtered count matrix.

To install scruff using devtools:

library(devtools)
install_github("compbiomed/scruff")

An introduction to scruff package is available within the package as a vignette which can be opened via running

vignette("scruff")

The following figures are generated using data from (Van den Brink et al. 2017) and scruff package.