Package: bcbioRNASeq
Title: bcbio RNA-Seq
Description: Toolkit for bcbio RNA-seq analysis.
Version: 0.3.29
Date: 2019-10-30
Authors@R: c(
    person(
        given = "Michael",
        family = "Steinbaugh",
        email = "mike@steinbaugh.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-2403-2221")
    ),
    person(
        given = "Lorena",
        family = "Pantano",
        email = "lorena.pantano@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0002-3859-3249")
    ),
    person(
        given = "Rory",
        family = "Kirchner",
        email = "roryk@alum.mit.edu",
        role = "aut",
        comment = c(ORCID = "0000-0003-4814-5885")
    ),
    person(
        given = "Victor",
        family = "Barrera",
        email = "barrera.vic@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0003-0590-4634")
    ),
    person(
        given = "Brad",
        family = "Chapman",
        email = "chapmanb@fastmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0002-3026-1856")
    ),
    person(
        given = "Mary",
        family = "Piper",
        email = "mary.piper@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0003-2699-3840")
    ),
    person(
        given = "Meeta",
        family = "Mistry",
        email = "meeta.mistry@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0002-5830-9479")
    ),
    person(
        given = "Radhika",
        family = "Khetani",
        email = "rkhetani@hsph.harvard.edu",
        role = "aut",
        comment = c(ORCID = "0000-0003-2430-2970")
    ),
    person(
        given = "Kayleigh",
        family = "Rutherford",
        email = "kayrut1@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0001-9699-2363")
    ),
    person(
        given = "Oliver",
        family = "Hofmann",
        email = "ohofmann72@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0002-7738-1513")
    ),
    person(
        given = "John",
        family = "Hutchinson",
        email = "jnhutchinson@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0002-7804-7576")
    ),
    person(
        given = "Shannan",
        family = "Ho Sui",
        email = "shosui@hsph.harvard.edu",
        role = "aut",
        comment = c(ORCID = "0000-0002-6191-4709")
    ),
    person(
        given = "Harvard Chan Bioinformatics Core",
        email = "bioinformatics@hsph.harvard.edu",
        role = c("cph", "fnd")
    ))
URL:
    https://bioinformatics.sph.harvard.edu/bcbioRNASeq/,
    https://github.com/hbc/bcbioRNASeq/
BugReports: https://github.com/hbc/bcbioRNASeq/issues/
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends:
    R (>= 3.6),
    SummarizedExperiment (>= 1.14),
    basejump (>= 0.11.20)
Imports:
    BiocGenerics (>= 0.30),
    DESeq2 (>= 1.24),
    S4Vectors (>= 0.22),
    acidplots (>= 0.2.16),
    bcbioBase (>= 0.6.10),
    bioverbs (>= 0.2.10),
    cowplot (>= 1.0),
    edgeR (>= 3.26),
    ggplot2 (>= 3.2),
    goalie (>= 0.4.0),
    rlang (>= 0.4),
    scales (>= 1.0),
    sessioninfo (>= 1.1),
    tximport (>= 1.12),
    methods,
    utils
Suggests:
    BiocStyle (>= 2.12),
    DEGreport (>= 1.20),
    DESeqAnalysis (>= 0.2.10),
    DOSE (>= 3.10),
    EnsDb.Hsapiens.v75 (>= 2.99),
    acidroxygen (>= 0.1.3),
    clusterProfiler (>= 3.12),
    hexbin (>= 1.27),
    knitr (>= 1.24),
    org.Hs.eg.db (>= 3.8),
    org.Mm.eg.db (>= 3.8),
    pathview (>= 1.24),
    patrick (>= 0.0.1),
    rhdf5 (>= 2.28),
    rmarkdown (>= 1.15),
    roxygen2 (>= 6.1),
    testthat (>= 2.2),
    tidyverse (>= 1.2),
    viridis (>= 0.5),
    vsn (>= 3.52)
Remotes:
    acidgenomics/DESeqAnalysis,
    acidgenomics/acidplots,
    acidgenomics/acidroxygen,
    acidgenomics/basejump,
    acidgenomics/bioverbs,
    acidgenomics/goalie,
    hbc/bcbioBase
biocViews:
    DataImport,
    DataRepresentation,
    DifferentialExpression,
    GeneExpression,
    QualityControl,
    ReportWriting,
    RNASeq,
    Transcription,
    Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
VignetteBuilder: knitr
