Package: bcbioRNASeq
Title: RNA-Seq Utilities
Description: Toolkit for bcbio RNA-seq analysis.
Version: 0.2.9
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: http://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: TRUE
Depends: R (>= 3.5), SummarizedExperiment, bcbioBase (== 0.4.1), DESeq2
        (>= 1.18)
Imports: assertive.base, assertive.files, assertive.numbers,
        assertive.properties, assertive.sets, assertive.strings,
        assertive.types, basejump (== 0.7.2), BiocGenerics, cowplot (>=
        0.9), DEGreport (>= 1.14), dplyr (>= 0.7), edgeR (>= 3.20),
        GenomicFeatures, ggplot2 (>= 3.0), ggrepel (>= 0.8), grid,
        knitr (>= 1.20), magrittr (>= 1.5), matrixStats, methods, readr
        (>= 1.1), reshape2 (>= 1.4), rlang (>= 0.2), rmarkdown (>=
        1.10), S4Vectors, scales, sessioninfo (>= 1.0), stringr (>=
        1.3), tibble (>= 1.4), tidyverse (>= 1.2), tximport (>= 1.6),
        utils, vsn
Suggests: BiocStyle, clusterProfiler (>= 3.8), DOSE (>= 3.6),
        EnsDb.Hsapiens.v75, org.Hs.eg.db, org.Mm.eg.db, pathview (>=
        1.20), roxygen2, testthat (>= 2.0), viridis
Remotes: acidgenomics/basejump@v0.7.2, hbc/bcbioBase@v0.4.1
biocViews: DataImport, DataRepresentation, DifferentialExpression,
        GeneExpression, QualityControl, ReportWriting, RNASeq,
        Transcription, Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Author: Michael Steinbaugh [aut, cre] (<https://orcid.org/0000-0002-2403-2221>),
  Lorena Pantano [aut] (<https://orcid.org/0000-0002-3859-3249>),
  Rory Kirchner [aut] (<https://orcid.org/0000-0003-4814-5885>),
  Victor Barrera [aut] (<https://orcid.org/0000-0003-0590-4634>),
  Brad Chapman [aut] (<https://orcid.org/0000-0002-3026-1856>),
  Mary Piper [aut] (<https://orcid.org/0000-0003-2699-3840>),
  Meeta Mistry [aut] (<https://orcid.org/0000-0002-5830-9479>),
  Radhika Khetani [aut] (<https://orcid.org/0000-0003-2430-2970>),
  Kayleigh Rutherford [aut] (<https://orcid.org/0000-0001-9699-2363>),
  Oliver Hofmann [aut] (<https://orcid.org/0000-0002-7738-1513>),
  John Hutchinson [aut] (<https://orcid.org/0000-0002-7804-7576>),
  Shannan Ho Sui [aut] (<https://orcid.org/0000-0002-6191-4709>),
  Harvard Chan Bioinformatics Core [cph, fnd]
Maintainer: Michael Steinbaugh <mike@steinbaugh.com>
Built: R 3.5.1; ; 2019-05-06 18:35:10 UTC; unix
