Department of Bioinformatics and Computational Biology

Software and Services Archive

From MD Anderson Bioinformatics
Jump to: navigation, search

Bioinformatics Software and Services Archives

Here is an archive of software and services developed by the Department of Bioinformatics and Computational Biology that are no longer supported and maintained. They 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.

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.
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.
Result Viewer is an application that allows investigators to browse the data analysis results of their microarray experiments.
Tissue microarrays are increasingly important tools that bring high-throughput technology to traditional pathology laboratories. Inmany cases, each spot on a tissue microarray is scored by a skilled pathologist and recorded manually. TAD consists of an Active ServerPage web interface to a relational SQL database that automatesrecording scores and linking them with clinical data for future interpretation.
The Cancer Genomic Atlas (TCGA) project studies different types of cancer by obtaining datasets from different tissue source sites, using different sequencing centers and technologies. Data sets can sometimes be biased depending on the batch from which it came. The TCGA Batch Effects Tool provides pre-computed graphical annotations of different TCGA data sets that allows users to screen for batch biases in the dataset. Use TCGA Batch Effects
Code to obtain MCMC samples for wavelet-based functional mixed model method in Morris and Carroll (2006). Obtains posterior samples of model parameters in functional mixed model. Original SiteDownload Package