recountWorkflow

 

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see recountWorkflow.

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

Bioconductor version: 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>

Installation

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

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

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

Documentation

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

browseVignettes("recountWorkflow")

 

HTML	R Script	recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor
Text		NEWS

Details

biocViews	ResourceQueryingWorkflow, Workflow
Version	1.4.2
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
Suggests Me
Links To Me

Package Archives

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

Source Package	recountWorkflow_1.4.2.tar.gz
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/
Package Downloads Report	Download Stats