Package: Rmmquant
Type: Package
Title: RNA-Seq multi-mapping Reads Quantification Tool
Version: 1.28.0
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: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        git make libharfbuzz-dev libbz2-dev libgit2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libtiff-dev libwebp-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:45:49 UTC
RemoteUrl: https://github.com/bioc/Rmmquant
RemoteRef: RELEASE_3_22
RemoteSha: 60d48d594a25ae16ad29a9870842b891446d64e8
NeedsCompilation: yes
Packaged: 2026-02-23 10:02:55 UTC; root
Author: Zytnicki Matthias [aut, cre]
Maintainer: Zytnicki Matthias <matthias.zytnicki@inra.fr>
Built: R 4.5.2; x86_64-w64-mingw32; 2026-02-23 10:06:07 UTC; windows
Archs: x64
