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GEOfastq

Downloads ENA Fastqs With GEO Accessions


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("GEOfastq")):

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

Details

biocViews DataImport, RNASeq, Software
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends
Imports xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
System Requirements
URL
Bug Reports https://github.com/alexvpickering/GEOfastq/issues
See More
Suggests BiocCheck, roxygen2, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me scfetch
Links To Me
Build Report Build Report

Package Archives

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

Source Package GEOfastq_1.10.0.tar.gz
Windows Binary GEOfastq_1.10.0.zip
macOS Binary (x86_64) GEOfastq_1.10.0.tgz
macOS Binary (arm64) GEOfastq_1.10.0.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