recount3
This is the released version of recount3; for the devel version, see recount3.
Explore and download data from the recount3 project
Bioconductor version: Release (3.23)
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]
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("recount3")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | SummarizedExperiment |
| Imports | BiocFileCache, data.table, GenomicRanges, httr, Matrix, methods, R.utils, rtracklayer, S4Vectors, sessioninfo, tools, utils |
| System Requirements | |
| URL | https://github.com/LieberInstitute/recount3 |
| Bug Reports | https://github.com/LieberInstitute/recount3/issues |
See More
| Suggests | BiocStyle, covr, knitcitations, knitr, lobstr, RefManageR, rmarkdown, testthat, 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | recount3_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | recount3_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | recount3_1.22.0.tgz |
| 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 |