recount
Explore and download data from the recount project
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") 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 | 1.32.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 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_1.32.0.tar.gz |
| Windows Binary (x86_64) | recount_1.32.0.zip |
| macOS Binary (x86_64) | recount_1.32.0.tgz |
| macOS Binary (arm64) | recount_1.32.0.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 |
| Old Source Packages for BioC 3.20 | Source Archive |