In order to enable more researchers to benefit from the method development in the R/Bioconductor-project (http://www.bioconductor.org), we have created the Chipster analysis software for microarray data. Chipster offers an intuitive graphical user interface to a comprehensive collection of up-to-date analysis methods.

Chipster supports all major DNA microarray platforms and, being a Java program, it is compatible with Windows, Linux and MacOS. The usual analysis features  such as preprocessing, statistical tests, clustering, and annotation are complemented with e.g. promoter analysis tools, bootstrapping hierarchical clustering results, and finding periodically expressed genes from time series data. Analysis history is automatically recorded, and the analysis scripts can be viewed at the source code level. Chipster can not only display images produced by the R/Bioconductor, but also produce interactive  visualizations for hierarchical and SOM clustering, scatter plots, histograms and time series plots. Users can freely choose different features of datasets to be plotted, such as log transformations of expression values.

Graphical client software runs at the user’s computer and connects to the CSC server environment through a front-end server. It is also possible to connect external Web Services to the system. The technical implementation is designed to maximize flexibility and minimize memory usage and data transfer between components.  New tools can be added using a simple annotation system, and no modifications or wrappers are needed. Analyser instances are pooled so that analysis requests can be processed as fast as possible. The client software utilizes Java Web Start to make installation and version updates as easy as possible.

Material

Introductory presentation (ppt)

Poster (pdf) 

Manual and tutorials

Analysis feature list

Contact information