TCGAbiolinksGUI

This package is for version 3.10 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see TCGAbiolinksGUI.

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

DOI: 10.18129/B9.bioc.TCGAbiolinksGUI

Bioconductor version: 3.10

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found in https://tcgabiolinksgui.shinyapps.io/tcgabiolinks/"

Author: Tiago Chedraoui Silva <tiagochst at gmail.com>, Antonio Colaprico <antonio.colaprico at ulb.ac.be>, Catharina Olsen <colsen at ulb.ac.be>, Michele Ceccarelli, Gianluca Bontempi <gbonte at ulb.ac.be>, Benjamin P. Berman <Benjamin.Berman at cshs.org>, Houtan Noushmehr <houtana at gmail.com>

Maintainer: Tiago C. Silva <tiagochst at gmail.com>

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

Installation

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


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

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("TCGAbiolinksGUI")

1. Introduction HTML R Script

2. Data menu HTML R Script

3. Analysis menu HTML

4. Integrative analysis menu HTML

5. Cases study HTML

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, DNASeq, DifferentialExpression, DifferentialMethylation, GUI, GeneExpression, GeneRegulation, Genetics, MethylationArray, Network, Pathways, Sequencing, Software, StatisticalMethod

Version 1.12.0

In Bioconductor since BioC 3.5 (R-3.4) (7 years)

License GPL (>= 3)

Depends R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data

Imports shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, maftools, stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER(>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks(>= 2.5.5), shinyjs (>= 0.7), colourpicker, sesame, shinyBS (>= 0.61)

System Requirements

URL

Suggests testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander

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Build Report Build Report

Package Archives

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

Source Package TCGAbiolinksGUI_1.12.0.tar.gz

Windows Binary TCGAbiolinksGUI_1.12.0.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) TCGAbiolinksGUI_1.12.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/TCGAbiolinksGUI

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TCGAbiolinksGUI

Bioc Package Browser https://code.bioconductor.org/browse/TCGAbiolinksGUI/

Package Short Url https://bioconductor.org/packages/TCGAbiolinksGUI/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.10 Source Archive