GEOfastq

DOI: 10.18129/B9.bioc.GEOfastq  

Downloads ENA Fastqs With GEO Accessions

Bioconductor version: Release (3.17)

GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA.

Author: Alex Pickering [cre, aut]

Maintainer: Alex Pickering <alexvpickering at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOfastq")

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("GEOfastq")

 

HTML	R Script	Using the GEOfastq Package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, RNASeq, Software
Version	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 years)
License	MIT + file LICENSE
Depends
Imports	xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
LinkingTo
Suggests	BiocCheck, roxygen2, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/alexvpickering/GEOfastq/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GEOfastq_1.8.0.tar.gz
Windows Binary	GEOfastq_1.8.0.zip
macOS Binary (x86_64)	GEOfastq_1.8.0.tgz
macOS Binary (arm64)	GEOfastq_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GEOfastq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GEOfastq
Bioc Package Browser	https://code.bioconductor.org/browse/GEOfastq/
Package Short Url	https://bioconductor.org/packages/GEOfastq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive