GNOSIS: An R Shiny app supporting cancer genomics survival analysis with cBioPortal

We have developed GNOSIS, an R Shiny App, incorporating a range of R packages enabling users to efficiently explore and visualise clinical and genomic data obtained from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels supporting a range of functionalities including data upload and initial exploration, data recoding and subsetting, multiple visualisations, survival analysis, statistical analysis and mutation analysis, in addition to facilitating reproducible research.

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GNOSIS Software Tool Article

The version of GNOSIS published in HRB Open Research can be found on the GNOSIS_Software_Tool_Article branch and initialised using:

shiny::runGitHub(repo = 'GNOSIS', username = 'Lydia-King', ref="GNOSIS_Software_Tool_Article")

Also available at: https://lydiaking.shinyapps.io/GNOSIS/

Can also be run by cloning repo on GNOSIS_Software_Tool_Article branch, navigating into repo and running server.R file.

GNOSIS Current Version

This version has integrated cBioPortalData() functions to allow users to select and analyse cBioPortal studies, in addition to manual upload.

The current version of GNOSIS can be installed and initialised using:

1. runGitHub

shiny::runGitHub(repo = 'GNOSIS', username = 'Lydia-King', ref="main")

2. via Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("GNOSIS")