DESCRIPTION

Package: srnadiff
Type: Package
Title: Finding differentially expressed unannotated genomic regions from RNA-seq
       data
Version: 1.19.2
Date: 2023-03-06
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
LazyData: false
Depends: R (>= 3.6)
SystemRequirements: C++11
Imports:
    Rcpp (>= 0.12.8),
    methods,
    devtools,
    S4Vectors,
    GenomeInfoDb,
    rtracklayer,
    SummarizedExperiment,
    IRanges,
    GenomicRanges,
    DESeq2,
    edgeR,
    baySeq,
    Rsamtools,
    GenomicFeatures,
    GenomicAlignments,
    grDevices,
    Gviz,
    BiocParallel,
    BiocStyle,
    BiocManager
LinkingTo: Rcpp
RoxygenNote: 7.1.1
biocViews: ImmunoOncology, 
    GeneExpression,
    Coverage,
    SmallRNA,
    Epigenetics,
    StatisticalMethod,
    Preprocessing,
    DifferentialExpression
Suggests: knitr,
    rmarkdown,
    testthat,
    BiocManager,
    BiocStyle
VignetteBuilder: knitr