GenomicDataCommons
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see GenomicDataCommons.
NIH / NCI Genomic Data Commons Access
Bioconductor version: 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 | ||
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 |
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 |