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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("recount")
In most cases, you don't need to download the package archive at all.
recount
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Explore and download data from the recount project
Bioconductor version: Release (3.5)
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 <lcollado at jhu.edu>
Citation (from within R,
enter citation("recount")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("recount")
Documentation
| HTML | R Script | Basic DESeq2 results exploration |
| HTML | R Script | recount quick start guide |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Coverage, DataImport, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.2.3 |
| In Bioconductor since | BioC 3.4 (R-3.3) (1 year) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.0), SummarizedExperiment |
| Imports | BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb, GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer(>= 1.35.3), S4Vectors, stats, utils |
| LinkingTo | |
| Suggests | AnnotationDbi, BiocStyle(>= 2.3.20), DESeq2, devtools (>= 1.6), EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6), org.Hs.eg.db, regionReport(>= 1.9.4), rmarkdown (>= 0.9.5), testthat |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/leekgroup/recount |
| BugReports | https://support.bioconductor.org/t/recount/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | recount_1.2.3.tar.gz |
| Windows Binary | recount_1.2.3.zip |
| Mac OS X 10.11 (El Capitan) | recount_1.2.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/recount |
| Package Short Url | http://bioconductor.org/packages/recount/ |
| Package Downloads Report | Download Stats |
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