Workflow Package: recountWorkflow

recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor

Bioconductor version: Development (3.8)

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.

Author: Leonardo Collado-Torres [aut, cre], Abhinav Nellore [ctb], Andrew E. Jaffe [ctb]

Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>

Citation (from within R, enter citation("recountWorkflow")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("recountWorkflow", version = "devel")

Documentation

To view available workflows for the version of this package installed in your system, start R and enter:

browseVignettes("recountWorkflow")

 

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Details

biocViews ResourceQueryingWorkflow, Workflow
Version 1.3.3
License Artistic-2.0
Depends R (>= 3.4.0)
Imports recount(>= 1.2.3), GenomicRanges, limma, edgeR, DESeq2, regionReport(>= 1.11.2), clusterProfiler(>= 3.5.5), org.Hs.eg.db(>= 3.4.1), gplots, derfinder, rtracklayer(>= 1.36.4), GenomicFeatures, bumphunter(>= 1.17.2), derfinderPlot
LinkingTo
Suggests BiocStyle(>= 2.5.19), BiocWorkflowTools, knitr, sessioninfo, rmarkdown, knitcitations
SystemRequirements
Enhances
URL https://github.com/LieberInstitute/recountWorkflow
BugReports https://support.bioconductor.org/t/recountWorkflow/
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