cbpManager

DOI: 10.18129/B9.bioc.cbpManager    

Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics

Bioconductor version: Release (3.14)

This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.

Author: Arsenij Ustjanzew [aut, cre, cph] , Federico Marini [aut]

Maintainer: Arsenij Ustjanzew <arsenij.ustjanzew at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("cbpManager")

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("cbpManager")

 

HTML	R Script	intro.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, GUI, ImmunoOncology, Preprocessing, Software, ThirdPartyClient, Visualization
Version	1.2.2
In Bioconductor since	BioC 3.13 (R-4.1) (1 year)
License	AGPL-3 + file LICENSE
Depends	shiny, shinydashboard
Imports	utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, markdown
LinkingTo
Suggests	knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://arsenij-ust.github.io/cbpManager/index.html
BugReports	https://github.com/arsenij-ust/cbpManager/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	cbpManager_1.2.2.tar.gz
Windows Binary	cbpManager_1.2.2.zip
macOS 10.13 (High Sierra)	cbpManager_1.2.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cbpManager
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cbpManager
Package Short Url	https://bioconductor.org/packages/cbpManager/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive