scruff

DOI: 10.18129/B9.bioc.scruff    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scruff.

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scruff")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scruff")

 

HTML	R Script	Process Single Cell RNA-Seq reads using scruff
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Technology, Visualization, WorkflowStep
Version	1.6.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0)
Imports	data.table, GenomicAlignments, GenomicFeatures, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/campbio/scruff/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scruff_1.6.0.tar.gz
Windows Binary	scruff_1.6.0.zip
macOS 10.13 (High Sierra)	scruff_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scruff
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scruff
Package Short Url	https://bioconductor.org/packages/scruff/
Package Downloads Report	Download Stats