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cbpManager

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

Bioconductor version: Release (3.17)

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 "4.3") 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")
intro.html HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, DataRepresentation, GUI, ImmunoOncology, Preprocessing, Software, ThirdPartyClient, Visualization
Version 1.8.4
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License AGPL-3 + file LICENSE
Depends shiny, shinydashboard
Imports utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown
Linking To
Suggests knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
System Requirements
Enhances
URL https://arsenij-ust.github.io/cbpManager/index.html
Bug Reports https://github.com/arsenij-ust/cbpManager/issues
See More
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_1.8.4.tar.gz
Windows Binary cbpManager_1.8.4.zip
macOS Binary (x86_64) cbpManager_1.8.4.tgz
macOS Binary (arm64) cbpManager_1.8.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/cbpManager
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cbpManager
Bioc Package Browser https://code.bioconductor.org/browse/cbpManager/
Package Short Url https://bioconductor.org/packages/cbpManager/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive