TCGAutils

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TCGAutils.

TCGA utility functions for data management


Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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

Details

biocViews Preprocessing, Software, WorkflowStep
Version 1.4.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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
System Requirements
URL
Bug Reports https://github.com/waldronlab/TCGAutils/issues
See More
Suggests BiocFileCache, BiocStyle, curatedTCGAData, devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr, magrittr, minfi, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox(>= 2.7.5), rtracklayer, R.utils, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To
Enhances
Depends On Me
Imports Me RTCGAToolbox
Suggests Me CNVRanger, curatedTCGAData, glmSparseNet
Links To Me
Build Report Build Report

Package Archives

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

Source Package TCGAutils_1.4.0.tar.gz
Windows Binary TCGAutils_1.4.0.zip
Mac OS X 10.11 (El Capitan) TCGAutils_1.4.0.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 3.9 Source Archive