leekgroup/recount: Explore and download data from the recount project

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Getting started

Package details

Bioconductor views Coverage DataImport DifferentialExpression GeneExpression RNASeq Sequencing Software
URL https://github.com/leekgroup/recount
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
leekgroup/recount documentation built on Nov. 5, 2018, 8:08 a.m.