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TCGAutils

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

TCGA utility functions for data management


Bioconductor version: Development (3.19)

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>

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

Installation

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

Details

biocViews DataImport, Preprocessing, Software, WorkflowStep
Version 1.23.4
In Bioconductor since BioC 3.7 (R-3.5) (6 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
See More
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 cBioPortalData, glmSparseNet, RTCGAToolbox, terraTCGAdata
Suggests Me CNVRanger, curatedTCGAData, dce, IntOMICS
Links To Me
Build Report Build Report

Package Archives

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

Source Package TCGAutils_1.23.4.tar.gz
Windows Binary TCGAutils_1.23.4.zip
macOS Binary (x86_64) TCGAutils_1.23.4.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