cbpManager

DOI: 10.18129/B9.bioc.cbpManager    

This is the development version of cbpManager; for the stable release version, see cbpManager.

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

Bioconductor version: Development (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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.2
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License AGPL-3 + file LICENSE
Depends shiny, shinydashboard
Imports utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs
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_1.1.2.tar.gz
Windows Binary cbpManager_1.1.2.zip
macOS 10.13 (High Sierra) cbpManager_1.1.2.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

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