CCMI - Presentation




9:00 AM-4:00 PM

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,, 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,, 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 and Motivation

9:20 am - Preparing Data for GenePattern

9:35 am - Running Analyses in GenePattern

10:10 am - Differential Analysis

10:35 am - Managing Job Results

10:55 am - Coffee Break

11:15 am - Pipelines

11:30 am - Gene Set Enrichment Analysis

Noon - Box Lunch Provided

1:00 pm - GenePattern Notebook introduction

1:25 pm - Clustering

1:50 pm - Class Prediction

2:15 pm - Coffee Break

2:30 pm - GenePattern Notebook Project: Samples and Features

3:15 pm - Other GenePattern Features

3:30 pm - Closing

3:35 pm - Open Q&A


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.

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