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Bioconductor - recount

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 (3.21)

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 (from within R, enter citation("recount")): Installation

To install this package, start R (version "4.5") 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")

Details biocViews Coverage, DataImport, DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software Version 1.34.0 In Bioconductor since BioC 3.4 (R-3.3) (8.5 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.

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