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March 2019: Automate your pathway enrichment analysis with R

Presenter: Paul Stewart

Meeting location

Date/time: Friday, March 15th @ 2pm

Location: Moffitt Stabile Research Building (SRB), David Murphey Conference Room (1st floor)

Meeting details

Pathway enrichment analysis is a common computational method for deriving biological meaning from large lists of genes. We will begin with a gentle introduction to the mathematical concepts used in pathway enrichment analysis. Next, we will discuss some practical considerations and the interpretation of results. Finally, we will use the R programming language to build a simple, reproducible pathway enrichment pipeline that can be used in your research.

Meeting prerequisites

  • A laptop with an internet connection.
  • Current versions of R and RStudio.
    • You will need to install the enrichR R package. To do this, first install R and RStudio. Next, open RStudio and find the "Console" window. In this window, type the command: install.packages('enrichR') and press enter. You might be prompted for a server to download from. They all contain the same libraries, so just pick one located in the United States.
  • Download the sample data. In most browsers, you can right click on this link and choose "Save As..." to save it to your hard drive.
  • Familiarity with R or any level experience with another programming language is a plus but not required. If you have never programmed before, then you might want to take a look at the first few sections in this tutorial before the meeting.

Meeting materials

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