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 http://cran.r-project.org/web/packages/Ckmeans.1d.dp/index.html

**CPX ^{2}** -- 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.

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