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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: