recount: Explore and download data from the recount project
Version 1.2.1

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.

Browse man pages Browse package API and functions Browse package files

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
Version1.2.1
URL https://github.com/leekgroup/recount
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("recount")

Man pages

abstract_search: Search the abstracts from the SRA studies available via the...
add_predictions: Add predicted phenotypes to a recount rse object
all_metadata: This function downloads the metadata for all projects.
browse_study: Open a SRA study id in the SRA website
coverage_matrix: Given a set of regions for a chromosome, compute the coverage...
download_study: Download data for a given SRA study id from the recount...
expressed_regions: Identify expressed regions from the mean coverage for a given...
find_geo: Find the GEO accession id for a given SRA run
geo_characteristics: Build a data.frame from GEO's charactersitics for a given...
geo_info: Extract information from GEO for a given sample
getRPKM: Compute an RPKM matrix based on a RangedSummarizedExperiment...
recount_abstract: Summary information at the project level for the recount...
recount_exons: Exon annotation used in recount
recount_genes: Gene annotation used in recount
recount-package: Explore and download data from the recount project.
recount_url: Files and URLs hosted by the recount project
reproduce_ranges: Reproduce the gene or exons used in the...
rse_gene_SRP009615: RangedSummarizedExperiment at the gene level for study...
scale_counts: Scale the raw counts provided by the recount project
snaptron_query: Query Snaptron to get data from exon-exon junctions present...

Functions

abstract_search Man page Source code
add_predictions Man page Source code
all_metadata Man page Source code
browse_study Man page Source code
coverage_matrix Man page Source code
download_study Man page Source code
expressed_regions Man page Source code
find_geo Man page Source code
geo_characteristics Man page Source code
geo_info Man page Source code
getRPKM Man page Source code
load_install Source code
read_pheno Source code
recount-package Man page
recount_abstract Man page
recount_exons Man page
recount_genes Man page
recount_url Man page
reproduce_ranges Man page Source code
rse_gene_SRP009615 Man page
scale_counts Man page Source code
snaptron_query Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/abstract_search.R
R/add_predictions.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/getRPKM.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/add_predictions.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/getRPKM.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
recount documentation built on May 20, 2017, 10:42 p.m.