RTCGA.CNV

DOI: 10.18129/B9.bioc.RTCGA.CNV  

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

CNV (Copy-number variation) datasets from The Cancer Genome Atlas Project

Bioconductor version: 3.17

Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.

Author: Przemyslaw Biecek <przemyslaw.biecek at gmail.com>

Maintainer: Marcin Kosinski <m.p.kosinski at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RTCGA.CNV")

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("RTCGA.CNV")

 

HTML	R Script	Using RTCGA to download CNV data as included in RTCGA.CNV
HTML	R Script	Using RTCGA to estimate ratio of MDM2 duplications
PDF		Reference Manual
Text		NEWS

Details

biocViews	AnnotationData, ExperimentData
Version	1.28.0
License	GPL-2
Depends	R (>= 3.3.0), RTCGA
Imports
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/RTCGA/RTCGA/issues
Depends On Me
Imports Me
Suggests Me	RTCGA
Links To Me
Build Report

Package Archives

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

Source Package	RTCGA.CNV_1.28.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RTCGA.CNV
Source Repository (Developer Access)	git clone [email protected]:packages/RTCGA.CNV
Package Short Url	https://bioconductor.org/packages/RTCGA.CNV/
Package Downloads Report	Download Stats