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("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 | ||
| 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 |