recountWorkflow

 

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

Bioconductor version: Release (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 <lcollado at jhu.edu>, Abhinav Nellore <anellore at gmail.com>, Andrew Jaffe <andrew.jaffe at libd.org>, E. Collado-Torres <lcollado at jhu.edu>

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

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("recountWorkflow", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Details

biocViews ResourceQueryingWorkflow, Workflow
Version 1.4.1
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/
Depends On Me
Imports Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/recountWorkflow
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/recountWorkflow
Package Short Url http://bioconductor.org/packages/recountWorkflow/
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