GenomicDataCommons

DOI: 10.18129/B9.bioc.GenomicDataCommons  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GenomicDataCommons.

NIH / NCI Genomic Data Commons Access

Bioconductor version: 3.17

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")):

Installation

To install this package, start R (version "4.3") 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 1.24.3
In Bioconductor since BioC 3.5 (R-3.4) (6.5 years)
License Artistic-2.0
Depends R (>= 3.4.0), magrittr
Imports stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr
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_1.24.3.tar.gz
Windows Binary GenomicDataCommons_1.24.3.zip (64-bit only)
macOS Binary (x86_64) GenomicDataCommons_1.24.3.tgz
macOS Binary (arm64) GenomicDataCommons_1.24.3.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

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