Package: recount3 1.23.0

Leonardo Collado-Torres

recount3: Explore and download data from the recount3 project

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

Authors:Leonardo Collado-Torres [aut, cre]

recount3_1.23.0.tar.gz
recount3_1.23.0.zip(r-4.7)recount3_1.23.0.zip(r-4.6)recount3_1.23.0.zip(r-4.5)
recount3_1.23.0.tgz(r-4.6-any)recount3_1.23.0.tgz(r-4.5-any)
recount3_1.23.0.tar.gz(r-4.7-any)recount3_1.23.0.tar.gz(r-4.6-any)
recount3_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
recount3/json (API)
NEWS

# Install 'recount3' in R:
install.packages('recount3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lieberinstitute/recount3/issues

On BioConductor:recount3-1.23.0(bioc 3.24)recount3-1.22.0(bioc 3.23)

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3

8.41 score 38 stars 284 scripts 900 downloads 2 mentions 21 exports 84 dependencies

Last updated from:454e04abfd. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE210
linux-devel-x86_64OK662
source / vignettesOK380
linux-release-x86_64OK638
macos-release-arm64OK594
macos-oldrel-arm64OK472
windows-develOK653
windows-releaseOK618
windows-oldrelOK567
wasm-releaseOK185

Exports:annotation_extannotation_optionsavailable_projectsavailable_samplescompute_read_countscompute_scale_factorscreate_hubcreate_rsecreate_rse_manualexpand_sra_attributesfile_retrieveis_paired_endlocate_urllocate_url_annproject_homesread_countsread_metadatarecount3_cacherecount3_cache_filesrecount3_cache_rmtransform_counts

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrhttr2IRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosessioninfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLXVectoryaml

recount3 quick start guide

Leonardo Collado-Torres

Rendered fromrecount3-quickstart.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-31
Started: 2020-04-14