GenomicDataCommons

DOI: 10.18129/B9.bioc.GenomicDataCommons  

NIH / NCI Genomic Data Commons Access

Bioconductor version: Release (3.16)

Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

Author: Martin Morgan [aut], Sean Davis [aut, cre], Marcel Ramos [ctb]

Maintainer: Sean Davis <seandavi at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomicDataCommons")

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("GenomicDataCommons")

 

HTML	R Script	Introduction to Accessing the NCI Genomic Data Commons
HTML	R Script	Questions and answers from over the years
HTML	R Script	Somatic Mutation Data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Sequencing, Software
Version	1.22.3
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), magrittr
Imports	stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/GenomicDataCommons http://github.com/Bioconductor/GenomicDataCommons http://bioconductor.github.io/GenomicDataCommons/
BugReports	https://github.com/Bioconductor/GenomicDataCommons/issues/new
Depends On Me
Imports Me	GDCRNATools, TCGAutils
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GenomicDataCommons_1.22.3.tar.gz
Windows Binary	GenomicDataCommons_1.22.3.zip (64-bit only)
macOS Binary (x86_64)	GenomicDataCommons_1.22.3.tgz
macOS Binary (arm64)	GenomicDataCommons_1.22.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicDataCommons
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomicDataCommons
Bioc Package Browser	https://code.bioconductor.org/browse/GenomicDataCommons/
Package Short Url	https://bioconductor.org/packages/GenomicDataCommons/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive