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GenomicDataCommons

NIH / NCI Genomic Data Commons Access


Bioconductor version: Release (3.18)

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")
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

Details

biocViews DataImport, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
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
See More
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
Links To Me
Build Report Build Report

Package Archives

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

Source Package GenomicDataCommons_1.26.0.tar.gz
Windows Binary GenomicDataCommons_1.26.0.zip (64-bit only)
macOS Binary (x86_64) GenomicDataCommons_1.26.0.tgz
macOS Binary (arm64) GenomicDataCommons_1.26.0.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