On June 29, 2010, GenePattern 3.2.3 was released, implementing a number of improvements to pipeline and job execution, as well as other fixes. See the release notes for more information.
A number of modules have been added to GenePattern since our September 2009 newsletter.
New modules
The following new modules have been added since September 2009:
- AuDIT provides an automated method of objectively evaluating multiple reaction monitoring-mass spectrometry (MRM-MS) data. It improves the overall accuracy of data analysis by identifying inaccurate transition data based on the presence of interfering signal or inconsistent recovery between replicate samples. AuDIT is based on work published by Abbatiello et al. in Automated Detection of Inaccurate and Imprecise Transitions in Peptide Quantification by Multiple Reaction Monitoring Mass Spectrometry (Clinical Chemistry, 2010).
- Circular Binary Segmentation (CBS) segments DNA copy number data into regions of estimated equal copy number using CBS, according to the methodology published by Olshen et al in Circular binary segmentation for the analysis of array-based DNA copy number data (Biostatistics, 2004).
- Cancer Profile Outlier Analysis (COPA) is used for finding recurrent chromosomal translocations in cancer. It uses microarray data to find pairs of genes with mutually
exclusive outlier tumor samples and either few or no outlier normal samples. This
implementation is an adaptation of the Bioconductor package copa by MacDonald (2006).
- CollapseDataset collapses Affymetrix multiple probe set expression values for a given gene into a single expression value. This eliminates multiple probes, which can inflate gene set enrichment scores, and facilitates the biological interpretation of gene set enrichment analysis results.
- ConvertToMAGETAB converts .gct or .res files to MAGE-TAB format.
- FLAMEContourDataGenerator creates the data needed to draw contour plots in the FLAMEViewer.
- GenePatternDocumentExtractor extracts GenePattern pipelines and data from a Word document created using the Word 2007 add-in for the GenePattern Reproducible Research Document (GRRD). The extracted pipelines can be installed and run on any GenePattern server. This module is useful for users who do not have Word 2007 and cannot otherwise access the pipelines provided in the Word document.
- MAGETABImportViewer converts files in MAGE-TAB format to file formats usable by GenePattern (.gct and .cls files).
- MetageneProjection implements the metagene projection methodology described by Tamayo et al (2007), allowing data sets to be compared in a lower-dimension metagene space and providing greater robustness to noise.
Updated modules
In addition, we have released updates to many existing modules. If you maintain your own GenePattern server, we recommend that you click Modules & Pipelines>Install from repository to download the updated modules.
Access the modules
The new and updated modules are available on the GenePattern Broad-hosted server (http://genepattern.broadinstitute.org/gp/), and are available for download (unless noted otherwise).
For comprehensive documentation on all modules in the repository, see the
Modules
page of the GenePattern web site.
The GenePattern team is looking for an experienced Java developer. For more information, see the job description at the Broad Institute Career Center.
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We always welcome your feedback and encourage you to send questions and comments to gp-help@broadinstitute.org.
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