GEOfastq
This is the development version of GEOfastq; for the stable release version, see GEOfastq.
Downloads ENA Fastqs With GEO Accessions
Bioconductor version: Development (3.24)
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.
Author: Alex Pickering [cre, aut]
Maintainer: Alex Pickering <alexvpickering at gmail.com>
citation("GEOfastq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GEOfastq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GEOfastq")| Using the GEOfastq Package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, RNASeq, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | xml2, rvest, stringr, RCurl, doParallel, foreach, plyr |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/alexvpickering/GEOfastq/issues |
See More
| Suggests | BiocCheck, roxygen2, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GEOfastq_1.21.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | GEOfastq_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | GEOfastq_1.21.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GEOfastq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GEOfastq |
| Bioc Package Browser | https://code.bioconductor.org/browse/GEOfastq/ |
| Package Short Url | https://bioconductor.org/packages/GEOfastq/ |
| Package Downloads Report | Download Stats |