ComputeOntario_Pathways_2025/0.0.Welcome_info.Rmd at master · BaderLab/ComputeOntario_Pathways_2025 · GitHub

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# Welcome <a id="welcome"></a>

Welcome to Bioinformatics for Pathway Enrichment Analysis - June 2025

## Meet your Faculty

### Veronique Voisin
Research Associate,<br> Donnelly Centre for Cellular and Biomolecular Research, <br>University of Toronto

<img src="./images/faculty/veronique_voisin.jpeg" style="float:right;width:125px;padding-left:10px;" />
Veronique is currently a bioinformatician applying pathway and networks analysis to high throughput genomics data for OICR cancer stem cell program. Previously, she worked on characterizing the gene signatures of different types of leukemias using a murine model

&nbsp;
&nbsp;

### Ruth Isserlin
Research data analyst,<br>Donnelly Centre for Cellular and Bimolecular Research, <br>University of Toronto

<img src="./images/faculty/ruth_isserlin.jpeg" style="float:left;width:125px;padding-right:10px;" />
Bioinformatician and data analyst in the Bader lab applying pathway and data analysis to varied data types. Developed Enrichment Map App for Cytoscape, an app to visually translate functional enrichment results from popular enrichment tools like GSEA to networks. Further developed the Enrichment Map Pipeline including development of additional Apps to help summarize and analyze resulting Enrichment Maps, including PostAnalysis, WordCloud, and AutoAnnotate App.


***

Thank you for attending the Bioinformatics for Pathway Enrichment Analysis
 workshop! Help us make this workshop better by filling out [our survey](https://forms.gle/D8w8qyJ1r71rFnZe9).

***


## Pre-Workshop Materials and Laptop Setup Instructions {#pre-workshop}

### Laptop Setup Instructions

A Check list to setup your laptop can be found [here](https://docs.google.com/forms/d/e/1FAIpQLSdknqfaPi-XJDeFwji5xga7rg-jdGiYsZWxW6zTCjjqbHcHsw/viewform?usp=sharing)

Install these tools on your laptop before coming to the workshop:

### Basic programs

  1. A robust text editor:
      * For Windows/PC - [notepad++](http://notepad-plus-plus.org/)
      * For Linux - [gEdit](http://projects.gnome.org/gedit/)
      * For Mac – [TextWrangler](http://www.barebones.com/products/textwrangler/download.html)

  1. A file decompression tool.
      * For Windows/PC – [7zip](http://www.7-zip.org/).
      * For Linux – [gzip](http://www.gzip.org).
      * For Mac – already there.

  1. A robust internet browser such as:
      * Firefox
      * Safari
      * Chrome
      * Microsoft Edge

  1. A PDF Viewer
      * Adobe Acrobat or equivalent

### Cytoscape Installation
Please install the latest version of [Cytoscape 3.10.3](https://github.com/cytoscape/cytoscape/releases/3.10.3/) or [Cytoscape Download](https://cytoscape.org/download.html) as well as a group of Cytoscape Apps that we will be using for different parts of the course.

  1. Install Cytoscape 3.10.3:
      * Go to: https://github.com/cytoscape/cytoscape/releases/3.10.3/ OR https://cytoscape.org/download.html
      * Choose the version corresponding to your operating system (OS, Windows or UNIX)
      * Follow instructions to install cytoscape
      * Verify that Cytoscape has been installed correctly by launching the newly installed application

  1. Install the following Cytoscape Apps - Apps are installed from within Cytoscape.
      * In order to install Apps launch Cytoscape
      * From the menu bar, select ‘Apps’, then ‘App Store’, then 'Show App Store'. ![](./images/cytoscape_app_menu.png)
      * App Store will appear in left hand Panel ![](./images/Cytoscape_app_manager.png)
      * Within search bar at the top of the panel, search for the app listed below.  Once you click on search icon a web browser will be launched with the apps that match your search.
      * Select the correct app (there might be a few that match your search term).
      * Click on "Install" ![](./images/app_store_download.png)
      * install the following:
          * EnrichmentMap 3.5.0
          * EnrichmentMap Pipeline Collection 1.1.0 (it will install ClusterMaker2 v2.3.4, WordCloud v3.1.4 and AutoAnnotate v1.5.0)
          * yFiles Layout Algorithms	1.1.4

### RStudio Installation
Please install the latest version of RStudio

  1. Download R and RStudio
      * Go to the [RStudio page](https://posit.co/download/rstudio-desktop/)
      * Locate the Download page and download the version corresponding to your system
          * MAC users:  https://download1.rstudio.org/electron/macos/RStudio-2025.05.0-496.dmg
          * Window users: https://download1.rstudio.org/electron/windows/RStudio-2025.05.0-496.exe
          * Unix users: https://download1.rstudio.org/electron/jammy/amd64/rstudio-2025.05.0-496-amd64.deb
      * Download and install R
      * Download and install RStudio
      * Launch RStudio to test it.

  1. Install required packages
      * fGSEA
      * GSA
      * gprofiler2
      * httr
      * RCurl
      * data.table
      * tidyverse
      * gpplot2
      * ggridges
      * webshot2
      * igraph
      * stringr
      * kableExtra
      * knitr
      * glue


## Pre-workshop Tutorials

It is in your best interest to complete these before the workshop.

### Cytoscape Preparation tutorials

Go to : https://github.com/cytoscape/cytoscape-tutorials/wiki and follow :

  * [Tour of Cytoscape](https://cytoscape.org/cytoscape-tutorials/protocols/tour-of-cytoscape/#/)
  * [Basic Data Visualization](https://cytoscape.org/cytoscape-tutorials/protocols/basic-data-visualization/#/)


### Pre-workshop Readings and Lectures

  1. Video Module 1 - [Introduction to Pathway and Network Analysis by Gary Bader](#intro)
  1. ***Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap*** Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD [Nat Protoc. 2019 Feb;14(2):482-517](https://www.nature.com/articles/s41596-018-0103-9) - [Available here as well](http://baderlab.org/Publications#EM_2019)

***

### Additional tutorials <a id="additionaltutorials"></a>

  * ***How to visually interpret biological data using networks*** Merico D, Gfeller D, Bader GD [Nature Biotechnology 2009 Oct 27, 921-924](https://www.nature.com/articles/nbt.1567)  - [Available here as well](http://baderlab.org/Publications#interpret_networks)

  * ***g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.*** Reimand J, Kull M, Peterson H, Hansen J, Vilo J   [Nucleic Acids Res. 2007 Jul;35](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933153/)

  * ***g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)*** Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, Vilo J [Nucleic Acids Res. 2019 May 8](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz369/5486750)

  * ***Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles*** Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP [Proc Natl Acad Sci U S A. 2005 Oct 25;102(43)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1239896/)

Interacting with Cytoscape using CyRest and command lines (for advanced users):
https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/R/advanced-cancer-networks-and-data-rcy3.Rmd