CCMI - Presentation

UCSF – Integrative Genomic Analysis with GenePattern

March

14

9:00 AM-5:00 PM

Slides from the workshop are now available for download here

Feel free to contact us (hello@ccmi.org) if you have trouble with access. 


Hosted by Michael Reich, Assistant Director of Bioinformatics, UC San Diego;
with presentations from John Liefeld and Edwin Francisco Juarez Rosales, UC San Diego. 

GenePattern, www.genepattern.org, enables researchers at all levels of computational expertise to use hundreds of tools for the analysis of gene expression, sequence variation, proteomics, and more, through an intuitive interface that requires no coding.

GenePattern makes reproducible research easy: analyses can be rerun at any time with the same inputs; every version of each tool is tracked, so that a result can be reproduced even if the code that produced it changes in the future; and researchers can chain analyses together to encapsulate and share their research as reproducible workflows.

A new GenePattern Notebook environment, www.genepattern-notebook.org, based on the popular Jupyter Notebook system, further allows users to interleave text, graphics, and analyses in unified "research narratives" that can be shared and published.

In this hands-on workshop, participants will learn how to:

  • Identify analyses relevant to their scientific objectives
  • Analyze and visualize gene expression (including RNA-seq) and other genomic data
  • Ensure that their analyses are reproducible
  • Create and publish research narratives that serve as a live, executable, sharable representation of a study
 

Tentative Schedule

  • 9:00 AM GenePattern Overview
  • 9:10 AM Introduction to GenePattern Notebook
  • 9:50 AM Data Preparation
  • 10:20 AM Jupyter Basics
  • 10:35 AM Using Python code and dataframes
  • 10:45 AM Coffee Break
  • 11:00 AM Differential Gene Expression Analysis
  • 11:45 AM Gene Set Enrichment Analysis (GSEA)
  • 12:15 PM Boxed Lunch Provided
  • 1:00 PM Clustering
  • 1:45 PM Dimension Reduction
  • 2:15 PM Classification and Prediction
  • 2:45 PM Coffee Break
  • 3:00 PM GenePattern Notebook and Python
  • 3:30 PM Integrative Genomics Viewer (IGV)
  • 3:45 PM Class Project
  • 4:30 PM Other GenePattern Features/Closing
 

No Show Policy
While we do not charge a fee to attend this event, these programs would not be sustainable and available to all wanting to attend, unless all registrants abide by the 48 hour cancellation notice policy. A no-show will also limit your ability to book our events in the future. Thank you in advance for your cooperation.

Pictures of Scientists Having Fun



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