Package: cbpManager 1.21.0

Arsenij Ustjanzew

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

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.

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

cbpManager_1.21.0.tar.gz
cbpManager_1.21.0.zip(r-4.7)cbpManager_1.21.0.zip(r-4.6)cbpManager_1.21.0.zip(r-4.5)
cbpManager_1.21.0.tgz(r-4.6-any)cbpManager_1.21.0.tgz(r-4.5-any)
cbpManager_1.21.0.tar.gz(r-4.7-any)cbpManager_1.21.0.tar.gz(r-4.6-any)
cbpManager_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cbpManager/json (API)

# Install 'cbpManager' in R:

install.packages('cbpManager', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/arsenij-ust/cbpmanager/issues

On BioConductor:cbpManager-1.21.0(bioc 3.24)cbpManager-1.20.0(bioc 3.23)

immunooncology dataimport datarepresentation gui thirdpartyclient preprocessing visualization cancer-genomics cbioportal clinical-data filegenerator mutation-data patient-data

5.51 score 8 stars 4 scripts 382 downloads 2 exports 81 dependencies

Last updated from:f2bfaa697f. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	176
linux-devel-x86_64	WARNING	316
source / vignettes	OK	268
linux-release-x86_64	WARNING	231
macos-release-arm64	WARNING	138
macos-oldrel-arm64	WARNING	112
windows-devel	WARNING	139
windows-release	WARNING	116
windows-oldrel	WARNING	129
wasm-release	OK	140

Exports:cbpManager setupConda_cbpManager

Dependencies:base64enc basilisk bit bit64 bslib cachem cli commonmark cpp11 crayon crosstalk digest dir.expiry dplyr DT evaluate fastmap filelock fontawesome fs generics glue here highr hms htmltools htmlwidgets httpuv jquerylib jsonlite knitr later lattice lazyeval lifecycle litedown magrittr markdown MASS Matrix memoise mime otel pander pillar pkgconfig plyr png prettyunits progress promises R6 rappdirs rapportools Rcpp RcppTOML reshape2 reticulate rintrojs rlang rmarkdown rprojroot sass shiny shinyBS shinycssloaders shinydashboard sourcetools stringi stringr tibble tidyselect tinytex tzdb utf8 vctrs vroom withr xfun xtable yaml

cbpManager: Managing cancer studies and generating files for cBioPortal

Rendered fromintro.rmdusingknitr::rmarkdown

Last update: 2021-11-26
Started: 2021-01-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Server logic of module for adding a column	addColumn_Server
UI elements of module for adding a column	addColumn_UI
Server logic of module for adding a row	addRow_Server
UI elements of module for adding a row	addRow_UI
Server logic of Resource tab module for adding a row	addRowRc_Server
UI elements of Resource tab module for adding a row	addRowRc_UI
Convert the cBioPortal sample- and patient-data file format into a data.frame	cBioPortalToDataFrame
Launch cbpManager	cbpManager
cbpManager	cbpManager-pkg
Check the input of dates	check_input_dates
Convert the data.frame to the appropriate file format for cBioPortal	convertDataFrame
Sanitize names	create_name
Server logic of module for deleting a column	deleteColumn_Server
UI elements of module for deleting a column	deleteColumn_UI
Server logic of module for removing a row	deleteRow_Server
UI elements of module for removing a row	deleteRow_UI
Server logic of Resource tab module for deleting a row	deleteRowRc_Server
UI elements of module for removing a row	deleteRowRc_UI
Server logic of module for editing a row	editRow_Server
UI elements of module for editing a row	editRow_UI
Server logic of Resource tab module for editing a row	editRowRc_Server
UI elements of module for editing a row	editRowRc_UI
Add empty column to a data.frame, if column does not exist in the data.frame	fncols
Create shiny UI-widget for specific columns of oncotree entries	generateOncotreeUIwidgets
Generate UI input widget	generateUIwidgets
Get Sample IDs associated with Patient IDs from the data_clinical_sample.txt file	getSampleIDs
Import patient data into current study data.frames	importPatientData
Check if input is in the appropriate date format	IsDate
Server logic of module for saving the resource data	saveResource_Server
UI elements of module for saving the resource data	saveResource_UI
Server logic of module for saving the source data	saveTimeline_Server
UI elements of module for saving the data	saveTimeline_UI
Install conda environment with basilisk before launching the app	setupConda_cbpManager
Shiny app server function	shinyAppServer
Shiny app server object create the shiny application user interface	shinyAppUI
Updates UI-widgets for specific columns of oncotree entries	updateOncotreeUIwidgets
Validate resource_definition input	validateResourceDefinition
Validate resource_patient input	validateResourcePatient
Validate resource_sample input	validateResourceSample
Validate resource_study input	validateResourceStudy
Validation Dependencies	.validation_dependencies ValidationDependencies
Write a line to a logfile containing the date, time, username (from Shinyproxy), and the name of the modified file.	writeLogfile