cbpManager

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see cbpManager.

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

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-1014-4521 , Federico Marini [aut] ORCID iD ORCID: 0000-0003-3252-7758

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, GUI, ImmunoOncology, Preprocessing, Software, ThirdPartyClient, Visualization

Version 1.16.0

In Bioconductor since BioC 3.13 (R-4.1) (4.5 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

System Requirements

URL https://arsenij-ust.github.io/cbpManager/index.html

Bug Reports https://github.com/arsenij-ust/cbpManager/issues

Suggests knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)

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 cbpManager_1.16.0.tar.gz

Windows Binary (x86_64) cbpManager_1.16.0.zip

macOS Binary (x86_64) cbpManager_1.16.0.tgz

macOS Binary (arm64) cbpManager_1.16.0.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/

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