Rmmquant

DOI: 10.18129/B9.bioc.Rmmquant    

This is the development version of Rmmquant; for the stable release version, see Rmmquant.

RNA-Seq multi-mapping Reads Quantification Tool

Bioconductor version: Development (3.9)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Rmmquant", version = "3.9")

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 1.1.0
License GPL-3
Depends R (>= 3.5)
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_1.1.0.tar.gz
Windows Binary Rmmquant_1.1.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) Rmmquant_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Rmmquant
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rmmquant
Package Short Url http://bioconductor.org/packages/Rmmquant/
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