TCGAutils

DOI: 10.18129/B9.bioc.TCGAutils    

TCGA utility functions for data management

Bioconductor version: Release (3.11)

A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable.

Author: Marcel Ramos [aut, cre], Lucas Schiffer [aut], Sean Davis [ctb], Levi Waldron [aut]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("TCGAutils")

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("TCGAutils")

 

HTML	R Script	TCGAutils Essentials
PDF		Reference Manual
Text		NEWS

Details

biocViews	Preprocessing, Software, WorkflowStep
Version	1.8.1
In Bioconductor since	BioC 3.7 (R-3.5) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment(>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
LinkingTo
Suggests	BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, RTCGAToolbox(>= 2.17.4), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL
BugReports	https://github.com/waldronlab/TCGAutils/issues
Depends On Me
Imports Me	cBioPortalData, RTCGAToolbox
Suggests Me	CNVRanger, curatedTCGAData, glmSparseNet, netDx
Links To Me
Build Report

Package Archives

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

Source Package	TCGAutils_1.8.1.tar.gz
Windows Binary	TCGAutils_1.8.1.zip
macOS 10.13 (High Sierra)	TCGAutils_1.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TCGAutils
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TCGAutils
Package Short Url	https://bioconductor.org/packages/TCGAutils/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive