Package: GEOfastq 1.21.0

Alex Pickering

GEOfastq: Downloads ENA Fastqs With GEO Accessions

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.

Authors:Alex Pickering [cre, aut]

GEOfastq_1.21.0.tar.gz
GEOfastq_1.21.0.zip(r-4.7)GEOfastq_1.21.0.zip(r-4.6)GEOfastq_1.21.0.zip(r-4.5)
GEOfastq_1.21.0.tgz(r-4.6-any)GEOfastq_1.21.0.tgz(r-4.5-any)
GEOfastq_1.21.0.tar.gz(r-4.7-any)GEOfastq_1.21.0.tar.gz(r-4.6-any)
GEOfastq_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
GEOfastq/json (API)
NEWS

# Install 'GEOfastq' in R:
install.packages('GEOfastq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/alexvpickering/geofastq/issues

On BioConductor:GEOfastq-1.21.0(bioc 3.24)GEOfastq-1.20.0(bioc 3.23)

rnaseqdataimportbioinformaticsfastqgene-expressiongeorna-seq

4.60 score 4 stars 9 scripts 346 downloads 5 exports 31 dependencies

Last updated from:b16140106c. Checks:1 WARNING, 6 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING146
linux-devel-x86_64OK247
source / vignettesOK279
linux-release-x86_64OK180
macos-release-arm64OK188
macos-oldrel-arm64OK163
windows-develERROR108
windows-releaseERROR100
windows-oldrelERROR114
wasm-releaseOK127

Exports:crawl_gsecrawl_gsmsextract_gsmsget_dldirget_fastqs

Dependencies:askpassbitopsclicodetoolscurldoParallelforeachgluehttriteratorsjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigplyrR6RcppRCurlrlangrvestselectrstringistringrsystibbleutf8vctrsxml2

Using the GEOfastq Package

Rendered fromGEOfastq.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2020-11-25
Started: 2020-10-26