cbpManager
Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cbpManager")Details
| Maintainer | Arsenij Ustjanzew <arsenij.ustjanzew@gmail.com> |
| Author | Arsenij Ustjanzew [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-1014-4521>), Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>) |
| License | AGPL-3 + file LICENSE |
| URL | https://arsenij-ust.github.io/cbpManager/index.html |
| Bug Reports | https://github.com/arsenij-ust/cbpManager/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, GUI, ImmunoOncology, Preprocessing, Software, ThirdPartyClient, Visualization |
| Package Short Url | https://bioconductor.org/packages/cbpManager/ |
Citation
From within R, enter citation("cbpManager"):
Arsenij Ustjanzew, Federico Marini. cbpManager: Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. doi:10.18129/B9.bioc.cbpManager, R package version 1.20.0, https://bioconductor.org/packages/cbpManager.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | cbpManager_1.20.0.tar.gz |
| Windows binary (x86_64) | cbpManager_1.20.0.zip |
| macOS binary (arm64) | cbpManager_1.20.0.tgz |
| macOS binary (x86_64) | cbpManager_1.20.0.tgz |
Dependencies
Depends: shiny, shinydashboard
Imports: utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite, rapportools, basilisk, reticulate, shinyBS, shinycssloaders, rintrojs, rlang, markdown
Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)