Software Packages

netDx [R]

General-purpose patient classifier that integrates multi-modal data and uses machine learning for feature selection.

• Available as BioConductor package or standalone Docker image
• Methods paper: Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD (2019). netDx: interpretable patient classification using integrated patient similarity networks. Mol Sys Biol 15:e8497
• Software paper: Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD (2021). netDx: Software for building interpretable patient classifiers by multi-‘omic data integration using patient similarity networks

IdeoViz [R]

Software to visualize statistical genomic data along a chromosomal ideogram.

• Available as Bioconductor package

Code from Published Papers

• Code archived in Zenodo for Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD (2019). netDx: interpretable patient classification using integrated patient similarity networks. Mol Sys Biol 15:e8497
• Github Repo for Pai S, Li P, Killinger B, Marshall L, Jia P, Liao J, Petronis A, Szabó PE, Labrie V. (2019). Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. Nat Comms. 10:2046.