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CFDE Virtual Workshop

Common Fund Data Ecosystem (CFDE) Virtual Workshop:

“Biomarker discovery from extracellular (cell-free) RNA-seq and tissue of origin from GTEx RNA-seq profiles”

Thursday September 12th 2024

1-3 pm ET / 10am-Noon PT

Requires Free Registration by September 9th (below)

Join us for an engaging hands-on workshop where Srimeenakshi (Meenu) Srinivasan of the Louise Laurent Lab at the University of California-San Diego will demonstrate how to perform integrative data analysis utilizing data from two Common Fund Data Ecosystem (CFDE) Data Coordinating Center portals followed by an interactive Q&A session.

The featured use case will illustrate biomarker discovery from extracellular cell-free RNA-seq data with tissue of origin identification through integrative analysis of GTEx tissue-derived RNA-seq data and plasma-derived small RNA-seq data from the ERCC exRNA Atlas.

To conduct workshop exercises in real time, attendees wishing to take part in the hands-on analysis will need to have the following installed prior to dialing into the workshop as there will not be time to conduct installations during the workshop.

  • Python (3.10 or greater)
  • R (4.2 or greater)
  • R packages (latest versions): 
    • data.table
    • tidyr
    • reshape2
    • dplyr
    • gdata DESeq2
    • BiocParallel
    • ggplot2
    • ggsignif

We also strongly encourage attendees to have Jupyter Notebook installed as well as this will be the platform used during the workshop. The Jupyter Notebook/files that will be used will be sent out via email.

Attendees who are not looking to conduct the analyses during the workshop are welcome to attend and observe.

A link to the virtual meeting will be provided in a confirmation email.

If you have any questions, please feel free to contact us at info@exrna.org

We look forward to seeing you there!

 

REGISTER HERE

 

To learn more about the projects & resources that will be discussed please see:

Common Fund Data Ecosystem (CFDE): https://commonfund.nih.gov/dataecosystem

Extracellular RNA Communication Consortium (ERCC):  https://exrna.org/

Genotype-Tissue Expression Project (GTEx): https://www.gtexportal.org/

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