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://biorxiv.org/content/early/2016/08/08/068478.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("recount")
AuthorLeonardo Collado-Torres [aut, cre], Abhinav Nellore [ctb], Andrew E. Jaffe [ctb], Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb], Kasper Daniel Hansen [ctb], Ben Langmead [ctb], Jeffrey T. Leek [aut, ths]
Bioconductor views Coverage DataImport DifferentialExpression GeneExpression RNASeq Sequencing Software
Date of publicationNone
MaintainerLeonardo Collado-Torres <lcollado@jhu.edu>
LicenseArtistic-2.0
Version1.0.17
https://github.com/leekgroup/recount

View on Bioconductor

Functions

abstract_search Man page
all_metadata Man page
browse_study Man page
coverage_matrix Man page
download_study Man page
expressed_regions Man page
find_geo Man page
geo_characteristics Man page
geo_info Man page
recount_abstract Man page
recount_exons Man page
recount_genes Man page
recount-package Man page
recount_url Man page
reproduce_ranges Man page
rse_gene_SRP009615 Man page
scale_counts Man page
snaptron_query Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/abstract_search.R R/all_metadata.R R/browse_study.R R/coverage_matrix.R R/download_study.R R/expressed_regions.R R/find_geo.R R/geo_characteristics.R R/geo_info.R R/recount-package.R R/recount_abstract-data.R R/recount_exons-data.R R/recount_genes-data.R R/recount_url-data.R R/reproduce_ranges.R R/rse_gene_SRP009615-data.R R/scale_counts.R R/snaptron_query.R R/utils.R
README.md
build
build/vignette.rds
data
data/datalist
data/recount_abstract.RData
data/recount_exons.RData
data/recount_genes.RData
data/recount_url.RData
data/rse_gene_SRP009615.RData
inst
inst/CITATION
inst/doc
inst/doc/SRP009615-results.R
inst/doc/SRP009615-results.Rmd
inst/doc/SRP009615-results.html
inst/doc/recount-quickstart.R
inst/doc/recount-quickstart.Rmd
inst/doc/recount-quickstart.html
man
man/abstract_search.Rd man/all_metadata.Rd man/browse_study.Rd man/coverage_matrix.Rd man/download_study.Rd man/expressed_regions.Rd man/find_geo.Rd man/geo_characteristics.Rd man/geo_info.Rd man/recount-package.Rd man/recount_abstract.Rd man/recount_exons.Rd man/recount_genes.Rd man/recount_url.Rd man/reproduce_ranges.Rd man/rse_gene_SRP009615.Rd man/scale_counts.Rd man/snaptron_query.Rd
tests
tests/test-all.R
tests/testthat
tests/testthat/test-annotation.R tests/testthat/test-data.R tests/testthat/test-misc.R tests/testthat/test-web-metadata.R
vignettes
vignettes/Makefile
vignettes/SRP009615-results.Rmd
vignettes/SRP009615-results.bib
vignettes/fakeVignettes
vignettes/fakeVignettes/SRP009615-results.Rmd
vignettes/recount-quickstart.Rmd

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