Package: srnadiff
Type: Package
Title: Finding differentially expressed unannotated genomic regions
        from RNA-seq data
Version: 1.33.0
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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:47:12 UTC
RemoteUrl: https://github.com/bioc/srnadiff
RemoteRef: HEAD
RemoteSha: 0a9f792b8c51367a5eaf63c3a90470739db4359b
NeedsCompilation: yes
Packaged: 2026-07-04 02:47:43 UTC; root
Author: Zytnicki Matthias [aut, cre],
  Gonzalez Ignacio [aut]
Maintainer: Zytnicki Matthias <matthias.zytnicki@inra.fr>