Note: This repository is no longer updated. Please go to https://github.com/campbio/scruff for latest updates.

scruff: Single Cell RNA-Seq UMI Filtering Facilitator

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.

Installation Instructions

To install scruff using devtools:

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

Package User Guide

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

vignette("scruff")

Example QC plots

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