scruff

DOI: 10.18129/B9.bioc.scruff    

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Bioconductor version: Release (3.8)

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, enter citation("scruff")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("scruff", version = "3.8")

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")

 

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

Details

biocViews Alignment, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Technology, Visualization, WorkflowStep
Version 1.0.0
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, refGenome, SingleCellExperiment, SummarizedExperiment
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, Rsubread, testthat
SystemRequirements
Enhances
URL
BugReports https://github.com/compbiomed/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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) scruff_1.0.0.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 http://bioconductor.org/packages/scruff/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: