recountWorkflow
This package is for version 3.9 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: 3.9
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 <lcolladotor at gmail.com>
citation("recountWorkflow")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor | HTML | R Script |
| NEWS | Text |
Details
| biocViews | ResourceQueryingWorkflow, Workflow |
| Version | 1.8.1 |
| 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 |
| System Requirements | |
| URL | https://github.com/LieberInstitute/recountWorkflow |
| Bug Reports | https://support.bioconductor.org/t/recountWorkflow/ |
See More
| Suggests | BiocStyle(>= 2.5.19), BiocWorkflowTools, knitr, sessioninfo, rmarkdown, knitcitations |
| Linking To | |
| Enhances | |
| 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_1.8.1.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 | https://bioconductor.org/packages/recountWorkflow/ |
| Package Downloads Report | Download Stats |