Package: srnadiff
Type: Package
Title: Finding differentially expressed unannotated genomic regions
        from RNA-seq data
Version: 1.31.0
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: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:43:01 UTC
RemoteUrl: https://github.com/bioc/srnadiff
RemoteRef: HEAD
RemoteSha: 680956dd3ec7f96dd5786690bcbf42ec7a90805e
NeedsCompilation: yes
Packaged: 2026-01-04 15:17:39 UTC; root
Author: Zytnicki Matthias [aut, cre],
  Gonzalez Ignacio [aut]
Maintainer: Zytnicki Matthias <matthias.zytnicki@inra.fr>
Built: R 4.6.0; x86_64-apple-darwin20; 2026-01-04 15:32:43 UTC; unix
