Package: GEOfastq 1.15.0

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_1.15.0.tar.gz
GEOfastq_1.15.0.zip(r-4.5)GEOfastq_1.15.0.zip(r-4.4)GEOfastq_1.15.0.zip(r-4.3)
GEOfastq_1.15.0.tgz(r-4.5-any)GEOfastq_1.15.0.tgz(r-4.4-any)GEOfastq_1.15.0.tgz(r-4.3-any)
GEOfastq_1.15.0.tar.gz(r-4.5-noble)GEOfastq_1.15.0.tar.gz(r-4.4-noble)
GEOfastq_1.15.0.tgz(r-4.4-emscripten)GEOfastq_1.15.0.tgz(r-4.3-emscripten)
GEOfastq.pdf |GEOfastq.html✨
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-1.15.0(bioc 3.21)GEOfastq-1.14.0(bioc 3.20)

rnaseqdataimportbioinformaticsfastqgene-expressiongeorna-seq

4.60 score 4 stars 6 scripts 260 downloads 5 exports 32 dependencies

Last updated 4 months agofrom:7ac929a894. Checks:5 OK, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-winERRORJan 29 2025
R-4.5-macOKJan 29 2025
R-4.5-linuxOKJan 29 2025
R-4.4-winERRORJan 29 2025
R-4.4-macOKJan 29 2025
R-4.3-winERRORJan 29 2025
R-4.3-macOKJan 29 2025

Exports:crawl_gsecrawl_gsmsextract_gsmsget_dldirget_fastqs

Dependencies:askpassbitopsclicodetoolscurldoParallelfansiforeachgluehttriteratorsjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigplyrR6RcppRCurlrlangrvestselectrstringistringrsystibbleutf8vctrsxml2

Using the GEOfastq Package

Rendered fromGEOfastq.Rmdusingknitr::rmarkdownon Jan 29 2025.

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