Package: recount3 1.17.0

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_1.17.0.tar.gz
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recount3.pdf |recount3.html✨
recount3/json (API)
NEWS

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

Peer review:

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

On BioConductor:recount3-1.17.0(bioc 3.21)recount3-1.16.0(bioc 3.20)

coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportannotation-agnosticbioconductorcountderfinderexongenehumanilluminajunctionmouserecountrecount3

7.91 score 31 stars 174 scripts 455 downloads 2 mentions 21 exports 85 dependencies

Last updated 13 days agofrom:1edc399fd6. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 11 2024
R-4.5-winOKDec 11 2024
R-4.5-linuxOKDec 11 2024
R-4.4-winOKDec 11 2024
R-4.4-macOKDec 11 2024
R-4.3-winOKDec 11 2024
R-4.3-macOKDec 11 2024

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:abindaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR.methodsS3R.ooR.utilsR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssessioninfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc

recount3 quick start guide

Leonardo Collado-Torres

Rendered fromrecount3-quickstart.Rmdusingknitr::rmarkdownon Dec 11 2024.

Last update: 2023-05-06
Started: 2020-04-14