DESCRIPTION

Package: regionReport
Type: Package
Title: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Version: 1.41.1
Date: 2025-01-14
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
    = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
    person(c("Andrew", "E."), "Jaffe", role = "aut",
    email = "andrew.jaffe@libd.org", comment = c(ORCID = "0000-0001-6886-1454")),
    person(c("Jeffrey", "T."), "Leek", role = c("aut", "ths"),
    email = "jtleek@gmail.com", comment = c(ORCID = "0000-0002-2873-2671")))
Description: Generate HTML or PDF reports to explore a set of regions such as
    the results from annotation-agnostic expression analysis of RNA-seq data at
    base-pair resolution performed by derfinder. You can also create reports for
    DESeq2 or edgeR results.
License: Artistic-2.0
LazyData: true
URL: https://github.com/leekgroup/regionReport
BugReports: https://support.bioconductor.org/t/regionReport/
VignetteBuilder: knitr
biocViews: DifferentialExpression, Sequencing, RNASeq, Software, Visualization,
    Transcription, Coverage, ReportWriting, DifferentialMethylation,
    DifferentialPeakCalling, ImmunoOncology, QualityControl
Depends:
    R(>= 3.2)
Imports:
    BiocStyle (>= 2.5.19),
    derfinder (>= 1.25.3),
    DEFormats,
    DESeq2,
    GenomeInfoDb,
    GenomicRanges,
    knitr (>= 1.6),
    knitrBootstrap (>= 0.9.0),
    methods,
    RefManageR,
    rmarkdown (>= 0.9.5),
    S4Vectors,
    SummarizedExperiment,
    utils
Suggests:
    BiocManager,
    biovizBase,
    bumphunter (>= 1.7.6),
    derfinderPlot (>= 1.29.1),
    sessioninfo,
    DT,
    edgeR,
    ggbio (>= 1.35.2),
    ggplot2,
    grid,
    gridExtra,
    IRanges,
    mgcv,
    pasilla,
    pheatmap,
    RColorBrewer,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    whisker
RoxygenNote: 7.2.3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)