GNOSIS

GNOSIS performs exploratory analysis of cancer consortia clinical and genomic data from the cBioPortal repository to identify prognostic markers using statistical and survival analyses.

Key Features:

• cBioPortal integration: Accesses cancer consortia clinical and genomic datasets curated by the cBioPortal repository.
• R Shiny implementation: Implemented in R using the Shiny framework.
• Data upload and exploration: Supports uploading clinical and genomic data for initial exploration.
• Data recoding and subsetting: Enables recoding and subsetting of datasets for tailored analyses and cohort selection.
• Data visualizations: Provides visualization options for interpreting clinical and genomic data.
• Statistical and survival analysis: Incorporates a range of R packages and survival analysis functionality to identify prognostic markers.
• Mutation analysis: Includes tools for analyzing somatic mutations and genomic alterations.
• Reproducibility support: Exports downloadable input logs and R scripts from each session to support reproducibility.

Scientific Applications:

• Prognostic biomarker discovery: Identification of novel genomic and clinical markers associated with patient survival using survival analysis.
• Integrative cancer genomics: Exploratory integration of clinical annotations and genomic data from cBioPortal for cohort-level analyses.
• Translational research and personalized medicine: Evaluation of genomic alterations in relation to clinical outcomes to inform diagnostic and therapeutic hypotheses.

Methodology:

Implemented in R with the Shiny framework, GNOSIS incorporates various R packages to perform statistical analyses and survival analysis, integrates cBioPortal-curated clinical and genomic datasets, supports data upload, recoding, subsetting, visualization and mutation analysis, and provides downloadable input logs and R scripts.