Rmmquant

DOI: 10.18129/B9.bioc.Rmmquant  

RNA-Seq multi-mapping Reads Quantification Tool

Bioconductor version: Release (3.16)

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.

Author: Zytnicki Matthias [aut, cre]

Maintainer: Zytnicki Matthias <matthias.zytnicki at inra.fr>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("Rmmquant")

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("Rmmquant")

 

HTML	R Script	The Rmmquant package
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Software, Transcription
Version	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges, SummarizedExperiment, devtools, TBX20BamSubset, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2, BiocStyle
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat
SystemRequirements	C++11
Enhances
URL
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	Rmmquant_1.16.0.tar.gz
Windows Binary	Rmmquant_1.16.0.zip
macOS Binary (x86_64)	Rmmquant_1.16.0.tgz
macOS Binary (arm64)	Rmmquant_1.16.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rmmquant
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rmmquant
Bioc Package Browser	https://code.bioconductor.org/browse/Rmmquant/
Package Short Url	https://bioconductor.org/packages/Rmmquant/
Package Downloads Report	Download Stats