Course Details

  • Date: February 8th, 2016 - February 8th, 2016
  • Time: 9:30 am - 4:30 pm
  • Location:
  • Presenter(s): Mary Goldman (UC Santa Cruz)

BTEP Workshop on Data Visualization, Exploration and Analysis

NOTE:This is a Bring Your Own Computer (BYOC) class, and will be simultaneously shared via GoToMeeting with attendees at the Advanced Technology Research Facility (ATRF) in Frederick, MD. Kindly select the location you plan to attend at the top of the registration page.

Date: February 8, 2016 (Monday)
Time: 9:30 am – 12:30 pm and 1:30 – 4:30 pm

Two Venues:

Live Workshop – NIH Bethesda – Bldg 10, FAES Room 3 (B1C207)
Remote Simulcast – ATRF, Room E1106 – 8560 Progress Dr, Frederick, MD

For more information on the Frederick simulcast, please contact:
Tracie Frederick, Technology Informationist, Scientific Library
Phone: 301-846-1094
Email: frederickt@mail.nih.gov


AGENDA

9:30 am – 12:30 pm – Data Visualization with UCSC Cancer Browser

Presenter: Mary Goldman

https://genome-cancer.ucsc.edu/

The Xena Platform from the UC Santa Cruz Genomics Institute integrates and visualizes functional genomics data from easy-to-use data hubs, allowing you to view data from large public datasets, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), as well as your own private secure data, together or separately. In this hands-on workshop we will view various -omic data types, including, but not limited to, positional mutation data, copy number variation, gene and exon expression, and phenotype/clinical data such as age and subtype. We will view example ‘private’ data in conjunction with public data from TCGA. We will dynamically generate KM plots as well as view data as a spreadsheet heatmap, bar graphs, and scatter plots. Xena is also integrated with Galaxy, giving access to a myriad of bioinformatics tools for analysis.


1:30 pm – 4:30 pm – Data Exploration with Qlucore

Presenter:  Sara Strandberg

Qlucore Omics Explorer is an exploration tools to analyze your experiment data yourself. It empowers biologists and bench scientists to easily visualize and analyze large numerical data sets such as Gene expression (array and RNA seq), DNA methylation, Proteomics, Metabolomics and Flow Cytometry data. Hand-outs and documentation will be provided to attendees on the day of workshop.

During the training you will learn how to:

1.     Import and visualize data with various plot types  – Heatmaps, PCA, Bar plots, Box plots, etc.

2.     Identify discriminating variables using statistical tests – t-test, ANOVA, regression analysis

3.     Use visualization to enhance the analysis and interpret results

4.     Achieve biological insight and work with hypothesis generation

5.     Export your result, such as variable lists and images

IMPORTANT!

Prior to the training please take the following steps.

1. Download and install the Qlucore software:

  • Go to www.qlucore.com/evaluation
  • Complete the quick registration process (if you do not have a login username/password)
  • Download and install the preferred version of the software (MAC or PC)

2. Activate Training License:

  • Save the license file provided below as Course Material 1 – QluCoreLicenseFile (qlucore_license_file.lic) on your Desktop
  • Open Qlucore Omics Explorer
  • Go to License/Import License File and select the license file that you just saved on Desktop

3. Download all of the files shared through the zipped file below – Course Material2: QlucoreTrainingMaterialsFeb82016