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Rmmquant

RNA-Seq multi-mapping Reads Quantification Tool


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("Rmmquant")):

Installation

To install this package, start R (version "4.3") 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")
The Rmmquant package HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, Software, Transcription
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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, apeglm, BiocStyle
System Requirements C++11
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Suggests knitr, rmarkdown, testthat
Linking To Rcpp
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Package Archives

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

Source Package Rmmquant_1.20.0.tar.gz
Windows Binary Rmmquant_1.20.0.zip
macOS Binary (x86_64) Rmmquant_1.20.0.tgz
macOS Binary (arm64) Rmmquant_1.20.0.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