TCGAutils

DOI: 10.18129/B9.bioc.TCGAutils  

TCGA utility functions for data management

Bioconductor version: Release (3.16)

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. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

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 "4.2") and enter:

if (!require("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	DataImport, Preprocessing, Software, WorkflowStep
Version	1.18.0
In Bioconductor since	BioC 3.7 (R-3.5) (5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment(>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
LinkingTo
Suggests	AnnotationHub, BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr, rmarkdown, 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, terraTCGAdata
Suggests Me	CNVRanger, curatedTCGAData, dce, glmSparseNet
Links To Me
Build Report

Package Archives

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

Source Package	TCGAutils_1.18.0.tar.gz
Windows Binary	TCGAutils_1.18.0.zip
macOS Binary (x86_64)	TCGAutils_1.18.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/TCGAutils
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TCGAutils
Bioc Package Browser	https://code.bioconductor.org/browse/TCGAutils/
Package Short Url	https://bioconductor.org/packages/TCGAutils/
Package Downloads Report	Download Stats