TCGAbiolinksGUI

This package is for version 3.7 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"


Bioconductor version: 3.7

"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 "3.5") 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

Details

biocViews DNAMethylation, DNASeq, DifferentialExpression, DifferentialMethylation, GUI, GeneExpression, GeneRegulation, Genetics, MethylationArray, Network, Pathways, Sequencing, Software, StatisticalMethod
Version 1.6.1
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, minfi, caret, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation27kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest, shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER(>= 2.0.0), clusterProfiler, parallel, TCGAbiolinks(>= 2.5.5), shinyjs (>= 0.7), colourpicker, shinyBS (>= 0.61)
System Requirements
URL
See More
Suggests testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package TCGAbiolinksGUI_1.6.1.tar.gz
Windows Binary TCGAbiolinksGUI_1.6.1.zip
Mac OS X 10.11 (El Capitan) TCGAbiolinksGUI_1.6.1.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 3.7 Source Archive