Software Developed at the Lab

ChiNet -- Pathway and subnetwork rewiring based on non-parametric discrete models.

Ckmeans.1d.dp -- an R package that performs distance-based clustering of one-dimensional data set. It achieves a similar purpose with the k-means algorithm. However, our algorithm guarantees optimality of the clustering returned. The k-means is heuristic and may not return an optimal clustering.

You can either install it directly from within R by

> install.packages("Ckmeans.1d.dp")

or download the package from CRAN at

CPX2 -- Comparative chi-square analysis of interactions. It is implemented as a program for comparative chi-square analysis of interactions across different molecular contexts. You can download and learn how to use it from its User Guide.

FunChisq -- The functional chi-square test used by NMSUSongLab and claimed a Best Performer in DREAM8 Network Inference Challenges. It is now available as package FunChisq from Comprehensive R Archive Network (CRAN). It is implemented as an R function for evaluating strength of funcational dependency without assuming a parametric functional form such as in linear regression. The function can be downloaded as FunChisq.R. An example using the test can be downloaded as FunChisq-example.R.

Q-method -- Pathway and subnetwork rewiring based on parametric linear and nonlinear differential equation models.

Joe Song

Last modified: Thu Apr 16 1:09:452 MDT 2015