• Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA...
• Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers
• Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place

Summary
The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists.

1. Running Analyses in GenePattern
2. Clustering
3. Prediction and Clasification
4. Working with analysis workflows: GenePattern pipelines
5. Working with Samples and Features
6. The GenePattern Notebook environment
7. Related tools: IGV, GSEA
8. Open Q&A

The data files, slides and exercises will be made available after the workshop.