GenomicDataCommons

This is the released version of GenomicDataCommons; for the devel version, see GenomicDataCommons.

NIH / NCI Genomic Data Commons Access

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DOI: 10.18129/B9.bioc.GenomicDataCommons

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Sequencing, Software

Version 1.34.1

In Bioconductor since BioC 3.5 (R-3.4) (8.5 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

Package Archives

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

Source Package GenomicDataCommons_1.34.1.tar.gz

Windows Binary (x86_64) GenomicDataCommons_1.33.1.zip (64-bit only)

macOS Binary (x86_64) GenomicDataCommons_1.33.1.tgz

macOS Binary (arm64) GenomicDataCommons_1.34.1.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

Old Source Packages for BioC 3.22 Source Archive