This is the development version of scruff; for the stable release version, see scruff.
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)Bioconductor version: Development (3.22)
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.
Author: Zhe Wang [aut, cre], Junming Hu [aut], Joshua Campbell [aut]
Maintainer: Zhe Wang <zhe at bu.edu>
Citation (from within R, entercitation("scruff")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scruff")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scruff")Follow Installation instructions to use this package in your R session.
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