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 <>
LicenseMIT + file LICENSE
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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scruff documentation built on Feb. 13, 2021, 2 a.m.