Package: recount
Title: Explore and download data from the recount project
Version: 1.39.0
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 (>= 3.5.0), 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)
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:43:58 UTC
RemoteUrl: https://github.com/bioc/recount
RemoteRef: HEAD
RemoteSha: a492ff2d6564d74d7208c79b49aa59320eb6675d
NeedsCompilation: no
Packaged: 2026-05-29 10:25:43 UTC; root
Author: Leonardo Collado-Torres [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2140-308X>),
  Abhinav Nellore [ctb],
  Andrew E. Jaffe [ctb] (ORCID: <https://orcid.org/0000-0001-6886-1454>),
  Margaret A. Taub [ctb],
  Kai Kammers [ctb],
  Shannon E. Ellis [ctb] (ORCID: <https://orcid.org/0000-0002-9231-0481>),
  Kasper Daniel Hansen [ctb] (ORCID:
    <https://orcid.org/0000-0003-0086-0687>),
  Ben Langmead [ctb] (ORCID: <https://orcid.org/0000-0003-2437-1976>),
  Jeffrey T. Leek [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-2873-2671>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>