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✨
DESCRIPTION |NEWS
card.svg |card.png
GEOfastq/json (API)

# 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)

rnaseq dataimport bioinformatics fastq gene-expression geo rna-seq

4.60 score 4 stars 10 scripts 5 exports 31 dependencies

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

Target	Result	Time
bioc-checks	WARNING	176
linux-devel-x86_64	OK	321
source / vignettes	OK	281
linux-release-x86_64	OK	227
macos-release-arm64	OK	108
macos-oldrel-arm64	OK	94
windows-devel	ERROR	110
windows-release	ERROR	103
windows-oldrel	ERROR	89
wasm-release	OK	177

Exports:crawl_gse crawl_gsms extract_gsms get_dldir get_fastqs

Dependencies:askpass bitops cli codetools curl doParallel foreach glue httr iterators jsonlite lifecycle magrittr mime openssl pillar pkgconfig plyr R6 Rcpp RCurl rlang rvest selectr stringi stringr sys tibble utf8 vctrs xml2

Using the GEOfastq Package

Installation | Overview of GEOfastq | Getting Started using GEOfastq | Session info

Rendered fromGEOfastq.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get GSE text from GEO	crawl_gse
Crawls SRX pages for each GSM to get metadata.	crawl_gsms
Extract GSMs needed to download RNA-seq data for a series	extract_gsms
Gets part of path to download bulk RNAseq sample from EBI or NCBI	get_dldir
Download and RNA-seq fastq data from EBI	get_fastqs