Single Cell RNA-seq UMI Filtering Facilitator
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README.md

README.md

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.

scruff total_reads

scruff aligned_reads

scruff gene_reads

scruff aligned_reads_fraction

scruff gene_reads_fraction_out_of_aligned_reads

scruff gene_reads_fraction_out_of_total_reads

scruff transcripts

scruff mt_transcripts

scruff mt_transcripts_fraction

scruff genes

scruff protein_coding_genes_fraction

scruff protein_coding_transcripts_fraction

scruff detection_power