Package: cbpManager 1.15.0

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]

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cbpManager.pdf |cbpManager.html✨
cbpManager/json (API)
NEWS

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

Peer review:

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

On BioConductor:cbpManager-1.13.0(bioc 3.20)cbpManager-1.12.0(bioc 3.19)

immunooncologydataimportdatarepresentationguithirdpartyclientpreprocessingvisualizationcancer-genomicscbioportalclinical-datafilegeneratormutation-datapatient-data

5.51 score 8 stars 1 scripts 154 downloads 2 exports 81 dependencies

Last updated 23 days agofrom:fd4e30c9aa. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:cbpManagersetupConda_cbpManager

Dependencies:base64encbasiliskbasilisk.utilsbitbit64bslibcachemclicommonmarkcpp11crayoncrosstalkdigestdir.expirydplyrDTevaluatefansifastmapfilelockfontawesomefsgenericsglueherehighrhmshtmltoolshtmlwidgetshttpuvjquerylibjsonliteknitrlaterlatticelazyevallifecyclemagrittrmarkdownMASSMatrixmemoisemimepanderpillarpkgconfigplyrpngprettyunitsprogresspromisesR6rappdirsrapportoolsRcppRcppTOMLreshape2reticulaterintrojsrlangrmarkdownrprojrootsassshinyshinyBSshinycssloadersshinydashboardsourcetoolsstringistringrtibbletidyselecttinytextzdbutf8vctrsvroomwithrxfunxtableyaml

cbpManager: Managing cancer studies and generating files for cBioPortal

Arsenij Ustjanzew

Rendered fromintro.rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Server logic of module for adding a columnaddColumn_Server
UI elements of module for adding a columnaddColumn_UI
Server logic of module for adding a rowaddRow_Server
UI elements of module for adding a rowaddRow_UI
Server logic of Resource tab module for adding a rowaddRowRc_Server
UI elements of Resource tab module for adding a rowaddRowRc_UI
Convert the cBioPortal sample- and patient-data file format into a data.framecBioPortalToDataFrame
Launch cbpManagercbpManager
cbpManagercbpManager-pkg
Check the input of datescheck_input_dates
Convert the data.frame to the appropriate file format for cBioPortalconvertDataFrame
Sanitize namescreate_name
Server logic of module for deleting a columndeleteColumn_Server
UI elements of module for deleting a columndeleteColumn_UI
Server logic of module for removing a rowdeleteRow_Server
UI elements of module for removing a rowdeleteRow_UI
Server logic of Resource tab module for deleting a rowdeleteRowRc_Server
UI elements of module for removing a rowdeleteRowRc_UI
Server logic of module for editing a roweditRow_Server
UI elements of module for editing a roweditRow_UI
Server logic of Resource tab module for editing a roweditRowRc_Server
UI elements of module for editing a roweditRowRc_UI
Add empty column to a data.frame, if column does not exist in the data.framefncols
Create shiny UI-widget for specific columns of oncotree entriesgenerateOncotreeUIwidgets
Generate UI input widgetgenerateUIwidgets
Get Sample IDs associated with Patient IDs from the data_clinical_sample.txt filegetSampleIDs
Import patient data into current study data.framesimportPatientData
Check if input is in the appropriate date formatIsDate
Server logic of module for saving the resource datasaveResource_Server
UI elements of module for saving the resource datasaveResource_UI
Server logic of module for saving the source datasaveTimeline_Server
UI elements of module for saving the datasaveTimeline_UI
Install conda environment with basilisk before launching the appsetupConda_cbpManager
Shiny app server functionshinyAppServer
Shiny app server object create the shiny application user interfaceshinyAppUI
Updates UI-widgets for specific columns of oncotree entriesupdateOncotreeUIwidgets
Validate resource_definition inputvalidateResourceDefinition
Validate resource_patient inputvalidateResourcePatient
Validate resource_sample inputvalidateResourceSample
Validate resource_study inputvalidateResourceStudy
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