Package: srnadiff
Type: Package
Title: Finding differentially expressed unannotated genomic regions
        from RNA-seq data
Version: 1.24.0
Date: 2024-03-07
Authors@R: c(
    person("Zytnicki", "Matthias", email = "matthias.zytnicki@inra.fr",
            role = c("aut", "cre")),
    person("Gonzalez", "Ignacio", role = "aut"))
Description: srnadiff is a package that finds differently expressed regions from
   RNA-seq data at base-resolution level without relying on existing annotation.
   To do so, the package implements the identify-then-annotate methodology that
   builds on the idea of combining two pipelines approachs differential
   expressed regions detection and differential expression quantification.
   It reads BAM files as input, and outputs a list differentially regions,
   together with the adjusted p-values.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.6)
SystemRequirements: C++11
Imports: Rcpp (>= 0.12.8), stats, methods, devtools, S4Vectors,
        GenomeInfoDb, rtracklayer, SummarizedExperiment, IRanges,
        GenomicRanges, DESeq2, edgeR, Rsamtools, GenomicFeatures,
        GenomicAlignments, grDevices, Gviz, BiocParallel, BiocManager,
        BiocStyle
LinkingTo: Rcpp
RoxygenNote: 7.2.3
biocViews: ImmunoOncology, GeneExpression, Coverage, SmallRNA,
        Epigenetics, StatisticalMethod, Preprocessing,
        DifferentialExpression
Suggests: knitr, rmarkdown, testthat, BiocManager, BiocStyle
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/srnadiff
git_branch: RELEASE_3_19
git_last_commit: 12aa125
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
NeedsCompilation: yes
Packaged: 2024-05-02 02:15:20 UTC; biocbuild
Author: Zytnicki Matthias [aut, cre],
  Gonzalez Ignacio [aut]
Maintainer: Zytnicki Matthias <matthias.zytnicki@inra.fr>
Built: R 4.4.0; x86_64-w64-mingw32; 2024-05-02 13:36:00 UTC; windows
Archs: x64
