October 2012 Java 6 update and GenePattern visualizer issues
Posted on Friday, October 26, 2012 at 02:47PM by David Eby
(Originally posted 2012-11-09)
Oracle recently released an update to their Java 6 platform which could cause problems for GenePattern users. The update disables the underlying technologies used by several …
GenePattern blog
Posted on Friday, October 26, 2012 at 01:49PM by David Eby
Welcome to the GenePattern blog! We are launching this as a place where we can post important news and announcements for the GenePattern community with more detail than can fit into a system announcement or tweet. Feel free to give us feedback and ask questions using the Comments section below …
Using ComparativeMarkerSelection for Differential Expression Analysis
Posted on Sunday, September 30, 2012 at 12:32PM by The GenePattern Team
Overview
In GenePattern, you use the ComparativeMarkerSelection module to identify the genes (if any) that are differentially expressed between two phenotype classes. Typically, this is a three-step process:
- Run the PreprocessDataset module to preprocess the expression data.
PreprocessDataset removes platform noise and genes that have little variation. It takes an …
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 …