recount-package: recount: Explore and download data from the recount project

In recount: Explore and download data from the recount project

Description

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.

Author(s)

Maintainer: Leonardo Collado-Torres [e-mail] (ORCID)

Authors:

• Jeffrey T. Leek [e-mail] (ORCID) [thesis advisor]

Other contributors:

• Abhinav Nellore [e-mail] [contributor]

• Andrew E. Jaffe [e-mail] (ORCID) [contributor]

• Margaret A. Taub [e-mail] [contributor]

• Kai Kammers [e-mail] [contributor]

• Shannon E. Ellis [e-mail] (ORCID) [contributor]

• Kasper Daniel Hansen [e-mail] (ORCID) [contributor]

• Ben Langmead [e-mail] (ORCID) [contributor]

See Also

Useful links:

• https://github.com/leekgroup/recount

• Report bugs at https://support.bioconductor.org/t/recount/

recount documentation built on Dec. 20, 2020, 2:01 a.m.