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.
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
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.
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.
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
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.