Qing-Song Xu | Search bioRxiv

bioRxiv2016

hdnom: Building Nomograms for Penalized Cox Models with High-Dimensional Survival Data

SummaryWe developed hdnom, an R package for survival modeling with high-dimensional data. The package is the first free and open-source software package that streamlines the workflow of penalized Cox model building, validation, calibration, comparison, and nomogram visualization, with nine types of penalized Cox regression methods fully supported. A web application and an online prediction tool maker are offered to enhance interac-tivity and flexibility in high-dimensional survival analysis.\n\nAvailabilityThe hdnom R package is available from CRAN: https://cran.r-project.org/package=hdnom under GPL. The hdnom web application can be accessed at http://hdnom.io. The web application maker is available from http://hdnom.org/appmaker. The hdnom project website: http://hdnom.org.\n\nContactqsxu@csu.edu.cn or miaozhu.li@duke.edu

Bioinformatics↗

bioRxiv2014

A phase diagram for gene selection and disease classification

Identifying a small subset of discriminate genes is important for predicting clinical outcomes and facilitating disease diagnosis. Based on the model population analysis framework, we present a method, called PHADIA, which is able to output a phase diagram displaying the predictive ability of each variable, which provides an intuitive way for selecting informative variables. Using two publicly available microarray datasets, its demonstrated that our method can selects a few informative genes and achieves significantly better or comparable classification accuracy compared to the reported results in the literature. The source codes are freely available at: www.libpls.net.

Bioinformatics↗