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Bioconductor - GEOfastq (development version)

This is the development version of GEOfastq; for the stable release version, see GEOfastq.

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-0002-6759

Maintainer: Alex Pickering <alexvpickering at gmail.com>

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GEOfastq")

For older versions of R, please refer to the appropriate Bioconductor release.

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GEOfastq")

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

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