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.

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]
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

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

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