GenePattern combines a powerful scientific workflow platform with more than 90 computational and visualization tools for the analysis of genomic data. GenePattern was developed by the Broad Institute - a collaboration of MIT, Harvard, and its affiliated hospitals and the WhiteHead Institute.
Features
- Analysis Pipelines: Create analysis workflows by chaining tasks together.
- Reproducible Research: Ensure that all versions of an analysis are available and its results are reproducible.
- Programming Environment: Call any GenePattern module from Java, MATLAB, or R.
Analyses
- Gene Expression Analysis: Standard and novel clustering, prediction, and marker selection methodologies.
- Proteomics: Peak detection, noise subtraction, peak matching, and more for advanced analysis of MALDI, SELDI, and LC-MS data.
- SNP Analysis: Analyze SNP microarrays using normalization, copy number estimation, smoothing, LOH determination, and visualization.
- Data Format Conversion: Import and export data, normalize and filter data, convert gene identifiers, and more.
This software is installed on a CCR server and accessed through a web interface currently available to UB and Roswell faculty/staff/students. The CCR installation is in the process of being tested. If you are interested in testing the software, please email CCR Help and we'll enable your account for GenePattern access.
If you have a GenePattern account with CCR, login here
NOTE: We STRONGLY recommend you use Firefox with GenePattern. There are known issues with Internet Explorer that might affect areas of the program you'd like to use. We are currently in contact with GenePattern support staff to develop workarounds for problems noticed when trying to add new modules. You must have at least Java 1.5 installed to use the GenePattern viewers.