GenomicDataCommons
NIH / NCI Genomic Data Commons Access
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.30.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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 |
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 | autonomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicDataCommons_1.30.0.tar.gz |
| Windows Binary (x86_64) | GenomicDataCommons_1.30.0.zip |
| macOS Binary (x86_64) | GenomicDataCommons_1.30.0.tgz |
| macOS Binary (arm64) | GenomicDataCommons_1.30.0.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 |