Package: srnadiff
Type: Package
Title: Finding differentially expressed unannotated genomic regions
        from RNA-seq data
Version: 1.29.1
Date: 2025-07-24
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, S4Vectors, Seqinfo,
        rtracklayer, SummarizedExperiment, IRanges, GenomicRanges,
        DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments,
        grDevices, Gviz, BiocParallel, BiocManager, BiocStyle
LinkingTo: Rcpp
RoxygenNote: 7.3.2
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: devel
git_last_commit: b23c87f
git_last_commit_date: 2025-07-24
Repository: Bioconductor 3.22
Date/Publication: 2025-07-25
NeedsCompilation: yes
Packaged: 2025-07-26 02:34:16 UTC; biocbuild
Author: Zytnicki Matthias [aut, cre],
  Gonzalez Ignacio [aut]
Maintainer: Zytnicki Matthias <matthias.zytnicki@inra.fr>
Built: R 4.5.1; x86_64-w64-mingw32; 2025-07-26 14:15:05 UTC; windows
Archs: x64
