GA4GHclient
This is the released version of GA4GHclient; for the devel version, see GA4GHclient.
A Bioconductor package for accessing GA4GH API data servers
Bioconductor version: Release (3.23)
GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.
Author: Welliton Souza [aut, cre], Benilton Carvalho [ctb], Cristiane Rocha [ctb]
Maintainer: Welliton Souza <well309 at gmail.com>
citation("GA4GHclient")):
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")
BiocManager::install("GA4GHclient")
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("GA4GHclient")| GA4GHclient | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, Software, ThirdPartyClient |
| Version | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0), S4Vectors |
| Imports | BiocGenerics, Biostrings, dplyr, Seqinfo, GenomicRanges, httr, IRanges, jsonlite, methods, VariantAnnotation |
| System Requirements | |
| URL | https://github.com/labbcb/GA4GHclient |
| Bug Reports | https://github.com/labbcb/GA4GHclient/issues |
See More
| Suggests | GenomeInfoDb, AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene |
| Linking To | |
| Enhances | |
| Depends On Me | GA4GHshiny |
| 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 | GA4GHclient_1.36.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | GA4GHclient_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | GA4GHclient_1.36.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GA4GHclient |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GA4GHclient |
| Bioc Package Browser | https://code.bioconductor.org/browse/GA4GHclient/ |
| Package Short Url | https://bioconductor.org/packages/GA4GHclient/ |
| Package Downloads Report | Download Stats |