Rmmquant
This is the released version of Rmmquant; for the devel version, see Rmmquant.
All Bioconductor versions of Rmmquant
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
RNA-Seq multi-mapping Reads Quantification Tool
Bioconductor version: 3.23 · Package version: 1.30.0
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"):
Zytnicki Matthias. Rmmquant: RNA-Seq multi-mapping Reads Quantification Tool. doi:10.18129/B9.bioc.Rmmquant, R package version 1.30.0, https://bioconductor.org/packages/Rmmquant.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.30.0 |
| License | GPL-3 |
| System Requirements | C++11 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 1466 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/Rmmquant/ |
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 | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | Rmmquant_1.30.0.tar.gz |
| Windows binary (x86_64) | Rmmquant_1.30.0.zip |
| macOS binary (arm64) | Rmmquant_1.30.0.tgz |
| macOS binary (x86_64) | Rmmquant_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rmmquant |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rmmquant |
| Package Downloads Report | Download Stats |
Dependencies
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
LinkingTo: Rcpp