TCGAutils

This is the development version of TCGAutils; for the stable release version, see TCGAutils.

TCGA utility functions for data management

Bioconductor version: Development (3.21)

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] (ORCID: ), Lucas Schiffer [aut], Sean Davis [ctb], Levi Waldron [aut]

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

Citation (from within R, enter citation("TCGAutils")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

TCGAutils Essentials	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Preprocessing, Software, WorkflowStep
Version	1.27.0
In Bioconductor since	BioC 3.7 (R-3.5) (6.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment(>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
System Requirements
URL
Bug Reports	https://github.com/waldronlab/TCGAutils/issues

Suggests	AnnotationHub, 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
Linking To
Enhances
Depends On Me
Imports Me	RTCGAToolbox, cBioPortalData, glmSparseNet, terraTCGAdata
Suggests Me	CNVRanger, dce, curatedTCGAData
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	TCGAutils_1.27.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
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