Package: Rmmquant
Type: Package
Title: RNA-Seq multi-mapping Reads Quantification Tool
Version: 1.31.0
Date: 2023-04-05
Authors@R: person("Zytnicki", "Matthias", email = "matthias.zytnicki@inra.fr",
  role = c("aut", "cre"))
Description: 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.
License: GPL-3
Encoding: UTF-8
SystemRequirements: C++11
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
RoxygenNote: 7.0.2
biocViews: GeneExpression, Transcription
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev git make libharfbuzz-dev libbz2-dev libgit2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev libssl-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:48:09 UTC
RemoteUrl: https://github.com/bioc/Rmmquant
RemoteRef: HEAD
RemoteSha: e4a76d6ccef094f60278e50cd7a6433d697f2a26
NeedsCompilation: yes
Packaged: 2026-06-18 11:24:15 UTC; root
Author: Zytnicki Matthias [aut, cre]
Maintainer: Zytnicki Matthias <matthias.zytnicki@inra.fr>