Archived Software

Below are archived software and services provided by the Department of Bioinformatics and Computational Biology. These 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. They 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 the Office of Technology Commercialization.

• BayesMix

  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.

• BREPA

  Breakpoint Resolution via Pairwise Alignment

• Cromwell

  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.

• MicroArray GO Browser

  GO Browser is a tool used for exploratory analysis of gene expression microarray data

• OOMPA

  OOMPA is an object-oriented microarray and proteomics analysis library implemented in R using S4 classes and compatible with BioConductor.

• Perfect Match

  The program analyzes oligonucleotides produced by Affymetrix Inc. It computes gene expression levels from files using a Positional Dependent Nearest Neighbor (PDNN) model.

• PRADA

  PRADA is a pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

• RATb

  The Report and Analysis Template Builder (RATb) uses XML and R to create reusable, structured Sweave files for the statistical and bioinformatic analysis of high-throughput omics datasets.

• Result Viewer

  Browser data base query tool for data analysis results of Microarray experiments.

• Rocket

  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.

• Sequence Quality Check

  This service provides a tool to predict whether sequences represent real genes with functional products or possibly contamination/transcriptional noise given either a sequence, or a list of sequences in FASTA format.

• TAD

  TAD consists of an Active Server Page web interface to a relational SQL database that automates tissue microarray recording scores and linking them with clinical data for future interpretation.

• TIGRA

  TIGRA: A Targeted Iterative Graph Routing Assembler for Breakpoint Assembly

• WFMM

  Wavelet-based functional mixed models. Implements Markov Chain Monte Carlo (MCMC) Bayesian wavelet-based functional mixed models procedure