Computing SNP Copy Number and Loss of Heterozygosity
Posted on Saturday, September 15, 2012 at 12:29PM by The GenePattern Team
Overview
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 …
Using IGV Through GenePattern
Posted on Thursday, August 30, 2012 at 12:23PM by The GenePattern Team
Overview
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 …
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 …