Package: easyRNASeq
Version: 2.47.0
Date: 2025-06-23
Type: Package
Title: Count summarization and normalization for RNA-Seq data
Author: Nicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler, Niklas Maehler
Maintainer: Nicolas Delhomme <nicolas.delhomme@umu.se>
Description: Calculates the coverage of high-throughput short-reads against
    a genome of reference and summarizes it per feature of interest (e.g. exon,
    gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq'
    or 'edgeR' package.
Imports:
    Biobase (>= 2.64.0),
    BiocFileCache (>= 2.12.0),
    BiocGenerics (>= 0.50.0),
    BiocParallel (>= 1.38.0),
    biomaRt (>= 2.60.1),
    Biostrings (>= 2.77.2),
    edgeR (>= 4.2.1),
    Seqinfo,
    genomeIntervals (>= 1.60.0),
    GenomicAlignments (>= 1.45.1),
    GenomicRanges (>= 1.61.1),
    SummarizedExperiment (>= 1.39.1),
    graphics,
    IRanges (>= 2.38.1),
    LSD (>= 4.1-0),
    methods,
    parallel,
    rappdirs (>= 0.3.3),
    Rsamtools (>= 2.25.1),
    S4Vectors (>= 0.42.1),
    ShortRead (>= 1.62.0),
    utils
Suggests:
    BiocStyle (>= 2.32.1),
    BSgenome (>= 1.72.0),
    BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0),
    curl,
    knitr,
    rmarkdown,
    RUnit (>= 0.4.33)
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
biocViews: GeneExpression, RNASeq, Genetics, Preprocessing, ImmunoOncology
RoxygenNote: 7.3.2
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/easyRNASeq
git_branch: devel
git_last_commit: 1cb9a73
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
