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recount
This is thedevelopment version of recount; for the stable release version, seerecount.
Explore and download data from the recount project
Bioconductor version: Development (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]
ORCID: 0000-0003-2140-308X, Abhinav Nellore [ctb], Andrew E. Jaffe [ctb] ORCID: 0000-0001-6886-1454, Margaret A. Taub [ctb], Kai Kammers [ctb], Shannon E. Ellis [ctb] ORCID: 0000-0002-9231-0481, Kasper Daniel Hansen [ctb] ORCID: 0000-0003-0086-0687, Ben Langmead [ctb] ORCID: 0000-0003-2437-1976, Jeffrey T. Leek [aut, ths] ORCID: 0000-0002-2873-2671
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("recount")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("recount")For older versions of R, please refer to the appropriateBioconductor 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 | 1.37.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 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
FollowInstallation instructions to use this package in your R session.
| Source Package | recount_1.37.0.tar.gz |
| Windows Binary (x86_64) | recount_1.37.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | recount_1.37.0.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 |