Software Developed at the Lab

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

Ckmeans.1d.dp -- A fast dynamic programming algorithm for optimal univariate clustering. Minimizing the sum of squares of within-cluster distances, the algorithm guarantees optimality and reproducibility. Its advantage over heuristic clustering algorithms in efficiency and accuracy is increasingly pronounced as the number of clusters k increases. With optional weights, the algorithm can also optimally segment time series and perform peak calling. An auxiliary function generates histograms that are adaptive to patterns in data. This package provides a powerful alternative to heuristic methods for univariate data analysis.

You can either install it directly from within R by

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

or download the package from CRAN at

Various versions of the package have been ported by third parties to MATLAB, JavaScript, Python, Ruby, SAS, and Scala.

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: Tue Jan 10 9:22:45 MST 2017