TCGAutils

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see TCGAutils.

TCGA utility functions for data management

Bioconductor version: 3.18

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 "4.3") 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")

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 1.22.2

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

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, RTCGAToolbox, terraTCGAdata

Suggests Me CNVRanger, curatedTCGAData, dce, glmSparseNet, IntOMICS

Links To Me

Build Report Build Report

Package Archives

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

Source Package TCGAutils_1.22.2.tar.gz

Windows Binary TCGAutils_1.22.2.zip

macOS Binary (x86_64) TCGAutils_1.22.2.tgz

macOS Binary (arm64) TCGAutils_1.22.2.tgz

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

Old Source Packages for BioC 3.18 Source Archive