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-4.4-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'))

Peer review:

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 218 downloads 5 exports 32 dependencies

Last updated 2 months agofrom:7ac929a894. Checks:OK: 4 ERROR: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winERRORNov 30 2024
R-4.5-linuxOKNov 30 2024
R-4.4-winERRORNov 30 2024
R-4.4-macOKNov 30 2024
R-4.3-winERRORNov 30 2024
R-4.3-macOKNov 30 2024

Exports:crawl_gsecrawl_gsmsextract_gsmsget_dldirget_fastqs

Dependencies:askpassbitopsclicodetoolscurldoParallelfansiforeachgluehttriteratorsjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigplyrR6RcppRCurlrlangrvestselectrstringistringrsystibbleutf8vctrsxml2

Using the GEOfastq Package

Rendered fromGEOfastq.Rmdusingknitr::rmarkdownon Nov 30 2024.

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