recount: Explore and download data from the recount project

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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.

Author
Leonardo 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]
Date of publication
None
Maintainer
Leonardo Collado-Torres <lcollado@jhu.edu>
License
Artistic-2.0
Version
1.0.6
URLs

View on Bioconductor

Man pages

abstract_search
Search the abstracts from the SRA studies available via the...
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
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...

Files in this package

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