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✨
DESCRIPTION |NEWS
card.svg |card.png
recount3/json (API)

# 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)

coverage differentialexpression geneexpression rnaseq sequencing software dataimport annotation-agnostic bioconductor count derfinder exon gene human illumina junction mouse recount recount3

8.45 score 39 stars 301 scripts 2 mentions 21 exports 84 dependencies

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

Target	Result	Time
bioc-checks	NOTE	213
linux-devel-x86_64	OK	651
source / vignettes	OK	444
linux-release-x86_64	OK	655
macos-release-arm64	OK	498
macos-oldrel-arm64	OK	408
windows-devel	OK	643
windows-release	OK	643
windows-oldrel	OK	585
wasm-release	OK	169

Exports:annotation_ext annotation_options available_projects available_samples compute_read_counts compute_scale_factors create_hub create_rse create_rse_manual expand_sra_attributes file_retrieve is_paired_end locate_url locate_url_ann project_homes read_counts read_metadata recount3_cache recount3_cache_files recount3_cache_rm transform_counts

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr fastmap filelock formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue httr httr2 IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig purrr R.methodsS3 R.oo R.utils R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo sessioninfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XML XVector yaml

recount3 quick start guide

Rendered fromrecount3-quickstart.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Obtain the file extension for a given organism and annotation	annotation_ext
List available annotation options for a given organism	annotation_options
List available projects in recount3	available_projects
List available samples in recount3	available_samples
Compute read counts	compute_read_counts
Compute count scaling factors	compute_scale_factors
Create UCSC track hub for BigWig files	create_hub
Create a recount3 RangedSummarizedExperiment gene or exon object	create_rse
Internal function for creating a recount3 RangedSummarizedExperiment object	create_rse_manual
Expand SRA attributes	expand_sra_attributes
Download a remote file and cache it to re-use later	file_retrieve
Guess whether the samples are paired end	is_paired_end
Construct the URL to access a particular 'recount3' file	locate_url
Construct the URL to a recount3 annotation file	locate_url_ann
Find available project home options	project_homes
Read a counts file	read_counts
Read the metadata files	read_metadata
Specify where to cache the recount3 files	recount3_cache
Locate recount3 cached files	recount3_cache_files
Remove recount3 cached files	recount3_cache_rm
Transform the raw counts provided by the recount3 project	transform_counts