PINSPlus: a tool for tumor subtype discovery in integrated genomic data.

ABSTRACT

SUMMARY: Since cancer is a heterogeneous disease, tumor subtyping is crucial for improved treatment and prognosis. We have developed a subtype discovery tool, called PINSPlus, that is (i) robust against noise and unstable quantitative assays, (ii) able to integrate multiple types of omics data in a single analysis and (iii) dramatically superior to established approaches in identifying known subtypes and novel subgroups with significant survival differences. Our validation on 12,158 samples from 44 datasets shows that PINSPlus vastly outperforms other approaches. The software is easy-to-use and can partition hundreds of patients in a few minutes on a personal computer. AVAILABILITY AND IMPLEMENTATION The package is available at https//cran.r-project.org/package=PINSPlus. Data and R script used in this manuscript are available at https//bioinformatics.cse.unr.edu/software/PINSPlus/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.