GenomicDataCommons

This is the development version of GenomicDataCommons; for the stable release version, see GenomicDataCommons.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

NIH / NCI Genomic Data Commons Access

Bioconductor version: Development (3.24)

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>

Citation (from within R, enter citation("GenomicDataCommons")):

Martin Morgan, Sean Davis. GenomicDataCommons: NIH / NCI Genomic Data Commons Access. doi:10.18129/B9.bioc.GenomicDataCommons, R package version 1.37.0, https://bioconductor.org/packages/GenomicDataCommons.

Generated from the package metadata; it may differ from the package's own citation.

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("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Sequencing, Software
Version	1.37.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0)
Imports	stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr
System Requirements
URL	https://bioconductor.org/packages/GenomicDataCommons http://github.com/Bioconductor/GenomicDataCommons http://bioconductor.github.io/GenomicDataCommons/
Bug Reports	https://github.com/Bioconductor/GenomicDataCommons/issues/new

Suggests	BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table
Linking To
Enhances
Depends On Me
Imports Me	GDCRNATools, TCGAutils
Suggests Me	autonomics, imageTCGA
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GenomicDataCommons_1.37.0.tar.gz
Windows Binary (x86_64)	GenomicDataCommons_1.37.0.zip
macOS Binary (big-sur-x86_64)	GenomicDataCommons_1.37.0.tgz
macOS Binary (sonoma-arm64)	GenomicDataCommons_1.37.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicDataCommons
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomicDataCommons
Package Short Url	https://bioconductor.org/packages/GenomicDataCommons/
Package Downloads Report	Download Stats