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.
- OOMPA is an object-oriented microarray and proteomics analysis
library implemented in R using S4 classes and compatible with
- SuperCurve is a stand-alone package, bundled with OOMPA, that
provides tools for the analysis of reverse phase protein arrays.
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
- 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
- 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
- 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
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