TCGAutils

DOI: 10.18129/B9.bioc.TCGAutils    

TCGA utility functions for data management

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TCGAutils", version = "3.8")

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 Preprocessing, Software, WorkflowStep
Version 1.2.1
License Artistic-2.0
Depends R (>= 3.5.0)
Imports AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges, methods, MultiAssayExperiment, RaggedExperiment(>= 1.5.7), rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
LinkingTo
Suggests BiocStyle, curatedTCGAData, devtools, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox(>= 2.7.5), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL
BugReports https://github.com/waldronlab/TCGAutils/issues
Depends On Me
Imports Me RTCGAToolbox
Suggests Me glmSparseNet
Links To Me
Build Report  

Package Archives

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

Source Package TCGAutils_1.2.1.tar.gz
Windows Binary TCGAutils_1.2.1.zip
Mac OS X 10.11 (El Capitan) TCGAutils_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/TCGAutils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TCGAutils
Package Short Url http://bioconductor.org/packages/TCGAutils/
Package Downloads Report Download Stats

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