DESCRIPTION

Package: recount
Title: Explore and download data from the recount project
Version: 1.33.0
Date: 2024-05-21
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
    email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
    person("Abhinav", "Nellore", role = "ctb",
    email = "anellore@gmail.com"), person(c("Andrew", "E."), "Jaffe",
    role = "ctb", email = "andrew.jaffe@libd.org",
    comment = c(ORCID = "0000-0001-6886-1454")), person(c("Margaret", "A."),
    "Taub", role = "ctb", email = "mtaub@jhsph.edu"), person("Kai", "Kammers",
    role = "ctb", email = "kai.kammers@gmail.com"), person(c("Shannon", "E."),
    "Ellis", role = "ctb", email = "sellis18@jhmi.edu",
    comment = c(ORCID = "0000-0002-9231-0481")), person(c("Kasper",
    "Daniel"), "Hansen", role = c("ctb"),
    email = "kasperdanielhansen@gmail.com",
    comment = c(ORCID = "0000-0003-0086-0687")), person("Ben", "Langmead",
    role = "ctb", email = 'langmea@cs.jhu.edu',
    comment = c(ORCID = "0000-0003-2437-1976")), person(c("Jeffrey", "T."),
    "Leek", role = c("aut", "ths"), email = "jtleek@gmail.com",
    comment = c(ORCID = "0000-0002-2873-2671")))
Depends:
    R (>= 3.3.0),
    SummarizedExperiment
Imports:
    BiocParallel,
    derfinder,
    downloader,
    GEOquery,
    GenomeInfoDb,
    GenomicRanges,
    IRanges,
    methods,
    RCurl,
    rentrez,
    rtracklayer (>= 1.35.3),
    S4Vectors,
    stats,
    utils
Suggests:
    AnnotationDbi,
    BiocManager,
    BiocStyle (>= 2.5.19),
    DESeq2,
    sessioninfo,
    EnsDb.Hsapiens.v79,
    GenomicFeatures,
    txdbmaker,
    knitr (>= 1.6),
    org.Hs.eg.db,
    RefManageR,
    regionReport (>= 1.9.4),
    rmarkdown (>= 0.9.5),
    testthat (>= 2.1.0),
    covr,
    pheatmap,
    DT,
    edgeR,
    ggplot2,
    RColorBrewer
VignetteBuilder: knitr
Description: Explore and download data from the recount project available at
    https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can
    download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level,
    the raw counts, the phenotype metadata used, the urls to the sample coverage
    bigWig files or the mean coverage bigWig file for a particular study. The
    RangedSummarizedExperiment objects can be used by different packages for
    performing differential expression analysis. Using
    http://bioconductor.org/packages/derfinder you can perform
    annotation-agnostic differential expression analyses with the data from the
    recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
URL: https://github.com/leekgroup/recount
BugReports: https://support.bioconductor.org/t/recount/
biocViews: Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing,
    Software, DataImport, ImmunoOncology
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)