recipe bioconductor-geofastq

Downloads ENA Fastqs With GEO Accessions

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/GEOfastq.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-geofastq/meta.yaml

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.

package bioconductor-geofastq

Versions:

1.6.0-0,  1.2.0-0,  1.0.0-0

Depends:

• r-base >=4.2,<4.3.0a0

• r-doparallel

• r-foreach

• r-plyr

• r-rcurl

• r-rvest

• r-stringr

• r-xml2

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-geofastq

and update with:

conda update bioconductor-geofastq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-geofastq:<tag>

(see bioconductor-geofastq/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-geofastq/README.html)