tRigon: an R package and Shiny App for integrative (path-)omics data analysis

Abstract

Background: Pathomics facilitates automated, reproducible and precise histopathology analysis and morphological phenotyping. Similar to molecular omics, pathomics datasets are high-dimensional, but also face large outlier variability and inherent data missingness, making quick and comprehensible data analysis challenging. To facilitate pathomics data analysis and interpretation as well as support a broad implementation we developed tRigon (Toolbox foR InteGrative (path-)Omics data aNalysis), a Shiny application for fast, comprehensive and reproducible pathomics analysis. Results: tRigon is available via the CRAN repository (https://cran.r-project.org/web/packages/tRigon) with its source code available on GitLab (https://git-ce.rwth-aachen.de/labooratory-ai/trigon). The tRigon package can be installed locally and its application can be executed from the R console via the command ‘tRigon::run_tRigon()’. Alternatively, the application is hosted online and can be accessed at https://labooratory.shinyapps.io/tRigon. We show fast computation of small, medium and large datasets in a low- and high-performance hardware setting, indicating broad applicability of tRigon. Conclusions: tRigon allows researchers without coding abilities to perform exploratory feature analyses of pathomics and non-pathomics datasets on their own using a variety of hardware.