campbio/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.

Getting started

Package details

Bioconductor views Alignment ImmunoOncology Preprocessing QualityControl RNASeq Sequencing SingleCell Software Technology Visualization WorkflowStep
LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
campbio/scruff documentation built on Nov. 16, 2021, 9:26 p.m.