scruff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.

Package details

AuthorZhe Wang [aut, cre], Junming Hu [aut], Joshua Campbell [aut]
Bioconductor views Alignment ImmunoOncology Preprocessing QualityControl RNASeq Sequencing SingleCell Software Technology Visualization WorkflowStep
MaintainerZhe Wang <[email protected]>
LicenseMIT + file LICENSE
Version1.0.1
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("scruff")

Try the scruff package in your browser

Any scripts or data that you put into this service are public.

scruff documentation built on Dec. 4, 2018, 6 p.m.