DESCRIPTION

Package: metaseqR2
Type: Package
Title: An R package for the analysis and result reporting
    of RNA-Seq data by combining multiple statistical
    algorithms
Authors@R: c(person(given="Panagiotis", family="Moulos",
    email="moulos@fleming.gr", role=c("aut", "cre")))
Depends:
    R (>= 4.0.0),
    DESeq2,
    limma,
    locfit,
    splines
Imports:
    ABSSeq,
    Biobase,
    BiocGenerics,
    BiocParallel,
    biomaRt,
    Biostrings,
    corrplot,
    DSS,
    DT,
    EDASeq,
    edgeR,
    genefilter,
    GenomeInfoDb,
    GenomicAlignments,
    GenomicFeatures,
    GenomicRanges,
    gplots,
    graphics,
    grDevices,
    harmonicmeanp,
    heatmaply,
    htmltools,
    httr,
    IRanges,
    jsonlite,
    lattice,
    log4r,
    magrittr,
    MASS,
    Matrix,
    methods,
    NBPSeq,
    pander,
    parallel,
    qvalue,
    rmarkdown,
    rmdformats,
    Rsamtools,
    RSQLite,
    rtracklayer,
    S4Vectors,
    stats,
    stringr,
    SummarizedExperiment,
    survcomp,
    txdbmaker,
    utils,
    VennDiagram,
    vsn,
    yaml,
    zoo
Suggests:
    BiocStyle,
    BiocManager,
    BSgenome,
    knitr,
    RMySQL,
    RUnit
Enhances:
    TCC
Description: Provides an interface to several normalization and
    statistical testing packages for RNA-Seq gene expression data.
    Additionally, it creates several diagnostic plots, performs
    meta-analysis by combinining the results of several statistical
    tests and reports the results in an interactive way.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: false
NeedsCompilation: yes
URL: http://www.fleming.gr
biocViews: Software, GeneExpression, DifferentialExpression, WorkflowStep,
    Preprocessing, QualityControl, Normalization, ReportWriting, RNASeq,
    Transcription, Sequencing, Transcriptomics, Bayesian, Clustering,
    CellBiology, BiomedicalInformatics, FunctionalGenomics, SystemsBiology,
    ImmunoOncology, AlternativeSplicing, DifferentialSplicing, 
    MultipleComparison, TimeCourse, DataImport, ATACSeq, Epigenetics,
    Regression, ProprietaryPlatforms, GeneSetEnrichment, BatchEffect,
    ChIPSeq
VignetteBuilder: knitr
BugReports: https://github.com/pmoulos/metaseqR2/issues
Version: 1.17.0
Date: 2024-03-13
Collate:
    'annotation.R'
    'argcheck.R'
    'count.R'
    'deseq.R'
    'export.R'
    'external.R'
    'filter.R'
    'json.R'
    'main.R'
    'meta.R'
    'noiseq.R'
    'norm.R'
    'metaseqr2-data.R'
    'metaseqR2-package.R'
    'plot.R'
    'query.R'
    'reportdb.R'
    'sim.R'
    'stat.R'
    'tracks.R'
    'util.R'
    'zzz.R'