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scruff

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 (3.19)

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 "4.4") 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.

Documentation

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

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

Details

biocViews Alignment, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Technology, Visualization, WorkflowStep
Version 1.21.1
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports data.table, GenomicAlignments, GenomicFeatures, txdbmaker, GenomicRanges, Rsamtools, ShortRead, parallel, plyr, BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio, rtracklayer, SingleCellExperiment, SummarizedExperiment, Rsubread, parallelly
System Requirements
URL
Bug Reports https://github.com/campbio/scruff/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scruff_1.21.1.tar.gz
Windows Binary scruff_1.21.1.zip (64-bit only)
macOS Binary (x86_64) scruff_1.21.1.tgz
macOS Binary (arm64) scruff_1.21.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/scruff
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scruff
Bioc Package Browser https://code.bioconductor.org/browse/scruff/
Package Short Url https://bioconductor.org/packages/scruff/
Package Downloads Report Download Stats