Upcoming Dates
One-day workshops will be held at the Broad Institute in
Cambridge, Massachusetts on
- February 4, Wednesday, 9am-5pm
- February 11, Wednesday, 9am-5pm
Register now. Academic/nonprofit organizations, free. For-profit organizations, $600.
If these dates are inconvenient, use the registration form to request
that we notify you of future workshops.
About the Workshop
Our popular GenePattern workshop introduces GenePattern and the methods behind the GenePattern modules for Gene Expression Analysis, including:
- Running analyses using the GenePattern web interface
- Differential gene expression analysis
- Classification/prediction methods
- Clustering
- Using pipelines to chain modules together to create and share methodologies
Request for Workshop Topics
What would you like to hear about in a future workshop? proteomics? SNP analysis? how to write modules? in-depth discussion of computational methods? Tell us what interests you:
We'd like to hear from you regardless of whether you've attended a workshop.
New Modules
A number of modules have been added to GenePattern since our February newsletter:
- CaArray2.1.0Importer imports data files from a caArray 2.1.0 repository into GenePattern. caArray (http://caarray.nci.nih.gov/) is a web-accessible array data management system developed by the National Cancer Institute Center for Bioinformatics (NCICB).
- ComBat runs the ComBat (Combining Batches) R script on a microarray dataset. The script uses an Empirical Bayes method to adjust for potential batch effects in the dataset. It is based on work published by Johnson, WE, Rabinovic, A, and Li, C in Adjusting batch effects in microarray expression data using Empirical Bayes methods (Biostatistics 8(1):118-127, 2007).
- GctToPcl and PclToGct convert between Stanford's PCL file format and GenePattern's GCT file format.
- GISTIC identifies regions of the genome that are significantly amplified or deleted across a set of samples. It implements the Genomic Identification of Significant Targets in Cancer (GISTIC) method published by Beroukhim R, Getz G, et al. in Assessing the significance of chromosomal abberations in cancer: Methodology and application to glioma (Proc Natl Acad Sci, 104:20007-20012, 2007). A GISTICPreprocess modules prepares SNP files for GISTIC and a Beroukhim.Getz.2007.PNAS.Glioma.GISTIC pipeline runs GISTIC with published data. The modules and pipeline are available only on the GenePattern public server.
- IGVPreprocessor preprocesses data for display in the Integrative Genomics Viewer (IGV, http://www.broad.mit.edu/igv). Preprocessing computes the data that will be displayed at selected zoom levels and stores the results in a smaller binary .h5 file. Most data files can be loaded into IGV without preprocessing. Available only on the GenePattern public server.
- IlluminaDASLPipeline creates a GenePattern GCT file from the raw data generated by a DNA-mediated
Annealing, Selection, extension and Ligation (DASL) assay (Illumina) and scanned
using a BeadArray Reader (Illumina). The pipeline comprises the IlluminaScanExtractor, IlluminaNormalizer, and IlluminaConcatenator modules. It implements the method published by Hoshida Y, et al. in Gene Expression in Fixed Tissues and Outcome in
Hepatocellular Carcinoma (N Engl J Med., 2008 Oct 15).
Available only on the GenePattern public server.
- SubMap and SubMapBrowser identify the correspondence or commonality of subtypes found in multiple, independent data sets generated on various platforms. They implement the Subclass Mapping method published by Hoshida Y, et al. in Subclass Mapping: Identifying Common Subtypes in Independent Disease Data sets (PLoS ONE 2(11): e1195, 2007).
- SurvivalCurve generates the survival curve for censored survival data. It is based on the survival 2.20 R package.
- SurvivalDifference tests whether there is a difference between two or more survival curves based on sample classes defined by genomic data. It is based on the survival 2.20 R package.
Updated Modules
In addition, the following modules have been updated:
Access the Modules
All new and updated modules are available on the GenePattern 3.1 public server:
http://genepattern.broad.mit.edu/gp.
To install new and updated modules on another GenePattern server,
open the GenePattern Web Client and click Modules & Pipelines>Install from Repository.
For comprehensive documentation on the modules in the repository, see our
module page.
If you've a GenePattern story to share, we'd love to hear about it.
If you're using GenePattern for your research, to share analysis methods,
or to publish analysis results, please let us know:
email the GenePattern team.
User Survey
We'd like to know more about your day-to-day experiences with GenePattern.
Our
user survey
is a brief online form that lets you give us feedback about the software and other aspects of using GenePattern.
Your responses are greatly appreciated - they help us to understand how GenePattern is being used and
how to make it a more valuable tool.
Early Adopters
If you'd like early access to new GenePattern releases to help us test new GenePattern features,
join the early adopters mailing list.
|
