Package: recountWorkflow
Title: recount workflow: accessing over 70,000 human RNA-seq samples
        with Bioconductor
Version: 1.36.0
Date: 2024-05-21
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
    email = "lcolladotor@gmail.com"), person("Abhinav", "Nellore", role = "ctb",
    email = "anellore@gmail.com"), person(c("Andrew", "E."), "Jaffe",
    role = "ctb", email = "andrew.jaffe@libd.org"))
Description: The recount2 resource is composed of over 70,000 uniformly
        processed human RNA-seq samples spanning TCGA and SRA,
        including GTEx. The processed data can be accessed via the
        recount2 website and the recount Bioconductor package. This
        workflow explains in detail how to use the recount package and
        how to integrate it with other Bioconductor packages for
        several analyses that can be carried out with the recount2
        resource. In particular, we describe how the coverage count
        matrices were computed in recount2 as well as different ways of
        obtaining public metadata, which can facilitate downstream
        analyses. Step-by-step directions show how to do a gene level
        differential expression analysis, visualize base-level genome
        coverage data, and perform an analyses at multiple feature
        levels. This workflow thus provides further information to
        understand the data in recount2 and a compendium of R code to
        use the data.
Depends: R (>= 3.6.0)
License: Artistic-2.0
Encoding: UTF-8
biocViews: Workflow, ResourceQueryingWorkflow
VignetteBuilder: knitr
Imports: recount, GenomicRanges, limma, edgeR, DESeq2, pheatmap,
        regionReport, clusterProfiler, org.Hs.eg.db, gplots, derfinder,
        GenomicState, bumphunter, derfinderPlot
Suggests: BiocStyle, BiocWorkflowTools, knitr, magick, sessioninfo,
        rmarkdown
NeedsCompilation: no
Workflow: true
URL: https://github.com/LieberInstitute/recountWorkflow
BugReports: https://support.bioconductor.org/t/recountWorkflow/
RoxygenNote: 7.2.3
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev
        libx11-dev xz-utils zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:43:06 UTC
RemoteUrl: https://github.com/bioc/recountWorkflow
RemoteRef: RELEASE_3_23
RemoteSha: 6ce0aaf55da837ec84d44daa78b0c92a6e5cf999
Packaged: 2026-10-04 17:14:38 UTC; root
Author: Leonardo Collado-Torres [aut, cre],
  Abhinav Nellore [ctb],
  Andrew E. Jaffe [ctb]
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>