This area of the web site will be used to store software tools that we are making publicly available. All tools are copyrighted by the University of Texas MD Anderson Cancer Center and by the individual employees of the cancer center who helped develop them. The tools are freely available for personal use in research projects; however, anyone wishing to use them or modify them for use in a commercial project should contact MD Anderson.

Available Software

OOMPA is an object-oriented microarray and proteomics analysis library implemented in R using S4 classes and compatible with BioConductor.
SuperCurve is a stand-alone package, bundled with OOMPA, that provides tools for the analysis of reverse phase protein arrays.
Wavelet-Based Functional Mixed Models
Code to obtain MCMC samples for wavelet-based functional mixed model method in Morris and Carroll (2004). Obtains posterior samples of model parameters in functional mixed model. Documentation is also available.
Cromwell is a set of MATLAB scripts for low-level processing of mass spectrometry proteomics data. Cromwell relies on the undecimated discrete wavelet transform for denoising spectra.
Choosing Thresholds for Cromwell
MATLAB code to produce visualizations as an aid to choosing reasonable thresholds for the Cromwell package.
A tool for exploratory analysis of gene expression microarray data.
Microarray GO Browser
An interactive tool for mapping microarray gene expression data onto the GeneOntology directed acyclic graph.
Perfect Match
A tool to quantify Affymetric microarrays. Quantifications are based on the "Position Dependent Nearest Neighbor" model, which makes explicit use of probe sequence information.
Tissue microarrays are increasingly important tools that bring high-throughput technology to traditional pathology laboratories. In many cases, each spot on a tissue microarray is scored by a skilled pathologist and recorded manually. TAD consists of an Active Server Page web interface to a relational SQL database that automates recording scores and linking them with clinical data for future interpretation.
Result Viewer is an application that allows investigators to browse the data analysis results of their microarray experiments.
Bayes Mix
A tool for performing model-based inference for differential gene expression, using a non-parametric Bayesian mixture probability model for the distribution of gene intensities under different conditions.
Rocket is a set of perl scripts and modules used to confirm that the clones sequenced in our Core Laboratory match the annotations provided by the supplier. (More precisely, Rocket provides a graphical interface using perl/Tk to a command line perl script.) Rocket will require some customization before you can use it. It assumes the existence of a local database containing the supplier's clone annotations; you'll have to create such a database separately and make sure the names of the fields in the database match those used by Rocket.

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