recount
This is the released version of recount; for the devel version, see recount.
Explore and download data from the recount project
Bioconductor version: Release (3.23)
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
Author: Leonardo Collado-Torres [aut, cre]
, Abhinav Nellore [ctb], Andrew E. Jaffe [ctb]
, Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb]
, Kasper Daniel Hansen [ctb]
, Ben Langmead [ctb]
, Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("recount")):
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("recount")
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("recount")| Basic DESeq2 results exploration | HTML | R Script |
| recount quick start guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.38.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0), SummarizedExperiment |
| Imports | BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer(>= 1.35.3), S4Vectors, stats, utils |
| System Requirements | |
| URL | https://github.com/leekgroup/recount |
| Bug Reports | https://support.bioconductor.org/t/recount/ |
See More
| Suggests | AnnotationDbi, BiocManager, BiocStyle(>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, txdbmaker, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap, DT, edgeR, ggplot2, RColorBrewer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | psichomics, RNAAgeCalc, recountWorkflow |
| Suggests Me | recount3 |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | recount_1.38.0.tar.gz |
| Windows Binary (x86_64) | recount_1.37.0.zip |
| macOS Binary (big-sur-x86_64) | recount_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | recount_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/recount |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/recount |
| Bioc Package Browser | https://code.bioconductor.org/browse/recount/ |
| Package Short Url | https://bioconductor.org/packages/recount/ |
| Package Downloads Report | Download Stats |