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RNA-Seq multi-mapping Reads Quantification Tool

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

The Rmmquant package HTML R Script
Reference Manual PDF


biocViews GeneExpression, Software, Transcription
Version 1.22.0
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,, DESeq2, apeglm, BiocStyle
System Requirements C++11
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Follow Installation instructions to use this package in your R session.

Source Package Rmmquant_1.22.0.tar.gz
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macOS Binary (x86_64) Rmmquant_1.22.0.tgz
macOS Binary (arm64) Rmmquant_1.22.0.tgz
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Source Repository (Developer Access) git clone
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