RTCGA.CNV

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

Bioconductor version: Release (3.20)

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>

Citation (from within R, enter citation("RTCGA.CNV")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationData, ExperimentData
Version	1.34.0
License	GPL-2
Depends	R (>= 3.3.0), RTCGA
Imports
System Requirements
URL
Bug Reports	https://github.com/RTCGA/RTCGA/issues

Suggests	knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	RTCGA
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	RTCGA.CNV_1.34.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RTCGA.CNV
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RTCGA.CNV
Package Short Url	https://bioconductor.org/packages/RTCGA.CNV/
Package Downloads Report	Download Stats