GenePattern Team Blog

Computing SNP Copy Number and Loss of Heterozygosity

Posted on Saturday, September 15, 2012 at 12:29PM by The GenePattern Team


In cancer genomics, copy number change is one of the hallmarks of the genetic instability common to most human cancers and loss of heterozygosity (LOH) of tumor suppressor genes is a crucial step in the development of sporadic and hereditary cancer (Monti, 2005). Using modules available in GenePattern, you can compute SNP copy number and LOH based on Affymetrix SNP chip data for paired target/normal samples and then view them in the Integrative Genomics Viewer (IGV). The following modules are used for this computation, with IGV at the end for viewing the results:

  • SNPFileCreator
  • XChromosomeCorrect
  • CopyNumberDivideByNormals
  • LOHPaired
  • IGV


SNPFileCreator converts the .CEL files from an Affymetrix array into a GenePattern .SNP file. Raw data for the probes in each SNP probe set are converted to a single intensity value per SNP using one of four modeling algorithms: Average Difference, PM/MM Difference Model (dChip, the default), Median Probe, or Trimmed Mean....

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Using IGV Through GenePattern

Posted on Thursday, August 30, 2012 at 12:23PM by The GenePattern Team


The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. Up until recently, this tool was only available outside of GenePattern, though it did accept GenePattern file formats. IGV can now be launched from a module available on the GenePattern Server or downloaded from the GenePattern Repository.

With this new development, users can pass their GenePattern result files directly to IGV through GenePattern.

IGV in GenePattern

The GenePattern IGV module launches the same application that is available from the IGV website. If you are a user of both the client IGV (either launching from the IGV website or your desktop) and GenePattern, this means you are using the same version of IGV complete with your preferences, home directory, saved genomes, and other such IGV saved presets. For all users,...

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Setting Up a Module Repository

Posted on Wednesday, July 11, 2012 at 12:33PM by The GenePattern Team

In this article we will go through the manual process of setting up your own module repository to connect to your GenePattern server. This may be desirable if you are developing many GenePattern modules and are looking for a way to control versions in both development and pre-release stages. This mechanism also allows for a centralized distribution of modules, both during development and at release.

The following steps describe the setup process:

  1. Download the following files:
  2. Put the properties file somewhere and remember the path.
    • Edit the URLs to that of the Tomcat you will run it in and the paths to where you would like the modules it serves to be stored.
    • Create the top level directories such that:
      • there is a directory for each of prod/dev and modules/suites/patches
      • the cache is the place the XML file (listing the modules) is stored in the file system
      • the prod.wi_ip_subnet and dev.wi_ip_subnet entries are changed to your...

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