recount3
This is the development version of recount3; for the stable release version, see recount3.
Explore and download data from the recount3 project
Bioconductor version: Development (3.21)
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.
Author: Leonardo Collado-Torres [aut, cre] (ORCID:
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("recount3")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("recount3")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("recount3")| recount3 quick start guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DataImport, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | Artistic-2.0 |
| Depends | SummarizedExperiment |
| Imports | BiocFileCache, methods, rtracklayer, S4Vectors, utils, httr, data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools |
| System Requirements | |
| URL | https://github.com/LieberInstitute/recount3 |
| Bug Reports | https://github.com/LieberInstitute/recount3/issues |
See More
| Suggests | BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown, testthat, pryr, interactiveDisplayBase, recount |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RNAseqQC |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | recount3_1.17.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/recount3 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/recount3 |
| Bioc Package Browser | https://code.bioconductor.org/browse/recount3/ |
| Package Short Url | https://bioconductor.org/packages/recount3/ |
| Package Downloads Report | Download Stats |