Package: bcbioRNASeq
Title: RNA-Seq Utilities
Description: Quality control and differential expression for bcbio RNA-seq and
    small RNA-seq experiments.
Version: 0.2.4
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 (>= 3.4), SummarizedExperiment, bcbioBase (>= 0.2.12),
        DESeq2 (>= 1.18)
Imports: BiocGenerics, DEGreport (>= 1.14), GenomicFeatures, S4Vectors,
        assertive.base, assertive.files, assertive.numbers,
        assertive.properties, assertive.sets, assertive.strings,
        assertive.types, basejump, cowplot, dplyr (>= 0.7), edgeR,
        ggplot2 (>= 2.2.1), ggrepel, grid, knitr, magrittr,
        matrixStats, methods, parallel, readr, reshape2, rmarkdown,
        rlang, scales, sessioninfo, stringr, tibble, tidyverse (>=
        1.2), tximport (>= 1.6), utils, vsn
Suggests: BiocStyle, DOSE, EnsDb.Hsapiens.v75, clusterProfiler,
        org.Hs.eg.db, org.Mm.eg.db, pathview, testthat
Remotes: hbc/bcbioBase, steinbaugh/basejump
biocViews: DataImport, DataRepresentation, DifferentialExpression,
        GeneExpression, QualityControl, ReportWriting, RNASeq,
        Transcription, Visualization
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.0.1
Author: Michael Steinbaugh [aut, cre] (0000-0002-2403-2221),
  Lorena Pantano [aut] (0000-0002-3859-3249),
  Rory Kirchner [aut] (0000-0003-4814-5885),
  Victor Barrera [aut] (0000-0003-0590-4634),
  Brad Chapman [aut] (0000-0002-3026-1856),
  Mary Piper [aut] (0000-0003-2699-3840),
  Meeta Mistry [aut] (0000-0002-5830-9479),
  Radhika Khetani [aut] (0000-0003-2430-2970),
  Kayleigh Rutherford [aut] (0000-0001-9699-2363),
  Oliver Hofmann [aut] (0000-0002-7738-1513),
  John Hutchinson [aut] (0000-0002-7804-7576),
  Shannan Ho Sui [aut] (0000-0002-6191-4709),
  Harvard Chan Bioinformatics Core [cph, fnd]
Maintainer: Michael Steinbaugh <mike@steinbaugh.com>
Built: R 3.4.1; ; 2018-06-11 12:08:10 UTC; unix
