Software

1. GO::TermFinder

GO::TermFinder comprises a set of Object-Oriented Perl modules, released under the MIT Open Source license, with a defined API that can be used for accessing information in the Gene Ontology and Gene Ontology associations files. In addition, the GO::TermFinder module itself can determine whether a set of genes is overrepresented with respect to their GO annotations than would be expected by chance if they had been drawn at random from a defined population of genes.

Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M. and Sherlock, G. (2004). GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.



2. The Stanford Microarray Database (SMD)

The entire set of code that underlies SMD is available for download under the MIT Open Source license. SMD is a scaleable microarray database with support for two-color data (from GenePix, Scanalyze and Agilent's FeatureExtraction program), and one color data, from Affymetrix GeneChips. Support also exists for CombiMatrix and Nimblegen arrays.

Hubble, J., Demeter, J., Jin, H., Mao, M., Nitzberg, M., Reddy, T.B., Wymore, F., Zachariah, Z.K., Sherlock, G. and Ball, C.A. (2009). Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res. 37, D898-D901.

Demeter, J., Beauheim, C., Gollub, J., Hernandez-Boussard, T., Jin, H., Maier, D., Matese, J.C., Nitzberg, M., Wymore, F., Zachariah, Z.K., Brown, P.O., Sherlock, G. and Ball, C.A. (2007). The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res. 35, D766-D770.

Ball, C.A., Awad, I.A.B, Demeter, J., Gollub, J., Hebert, J., Hernandez-Boussard, T., Jin, H., Matese, J.C., Nitzberg, M., Wymore, F., Zachariah, Z., Brown, P.O. and Sherlock, G. (2005). The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Research 33, D580-D582.



3. XCluster

XCluster performs agglomerative hierarchical clustering using centroid linkage. It is a command line application written in C, and readily compiles on most Unix systems (including MacOSX). The main feature of XCluster that distinguishes it from some other clustering programs is that it is fast, and memory efficient. XCluster can also do k-means clustering and make Self-Organizing Maps. See the XCluster page for more details.

4. Caryoscope

Caryoscope is a reusable Java UI component -- and a set of parsing utilities; command line tools and an application GUI -- for viewing gene expression data in a whole-genome context. Caryoscope is released under the MIT Open Source license.

Awad, I.A.B, Rees, C.A., Hernandez-Boussard, T., Ball, C.A. and Sherlock, G. (2004). Caryoscope: An Open Source Java Application for Viewing Microarray Data in a Genomic Context. BMC Bioinformatics 5:151.


5. GeneXplorer

GeneXplorer is a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. The software is released under the permissive MIT Open Source license.

Rees, C.A., Demeter, J., Matese, J.C., Botstein, D. and Sherlock, G. (2004). GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics 5:41.