GenomicDataCommons

DOI: 10.18129/B9.bioc.GenomicDataCommons    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see GenomicDataCommons.

NIH / NCI Genomic Data Commons Access

Bioconductor version: 3.14

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

Author: Martin Morgan [aut], Sean Davis [aut, cre]

Maintainer: Sean Davis <seandavi at gmail.com>

Installation

To install this package, start R (version "4.1") 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	1.18.0
In Bioconductor since	BioC 3.5 (R-3.4) (5 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), magrittr
Imports	stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment, S4Vectors, tibble
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/GenomicDataCommons http://github.com/Bioconductor/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_1.18.0.tar.gz
Windows Binary	GenomicDataCommons_1.18.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	GenomicDataCommons_1.18.0.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