Installation instructions

Day 1

Please install the following tools (available on all platforms):

• PathVisio requires the installation of Java 8 - you might need to create an Oracle account (free) before you can download it.
• PathVisio v3.3.0

Download the following databases:

• BridgeDb human mapping databases - Overiew
  • Download the database for Homo sapiens: Hs_Derby_Ensembl_105.bridge
  • Download the metabolites database: metabolites_20210109.bridge

Day 2

Please install the following tools (available on all platforms):

• Cytoscape v3.9.1

Open Cytoscape and go to App > App Manager

• Install the WikiPathways app
• Install the CyTargetLinker app
• Install the stringApp
• Install the clusterMaker2 app

Day 3

Please install the following tools (available on all platforms):

• R v4.2.1
• RStudio

Install required R-packages**

Open RStudio after installing R and RStudio and install BioCManager and required packages (you can copy the code and run it in RStudio)

install.packages("BiocManager")
BiocManager::install("RCy3") 
BiocManager::install("rWikiPathways") 
BiocManager::install("clusterProfiler") 
BiocManager::install("org.Hs.eg.db") 
BiocManager::install("RColorBrewer") 
BiocManager::install("EnhancedVolcano") 
BiocManager::install("dplyr") 
BiocManager::install("tidyverse") 
BiocManager::install("clusterProfiler") 
BiocManager::install("DESeq2") 

install.packages("rstudioapi") 
install.packages("readr") 
install.packages("data.table")

Contact

Feel free to contact us in case you have problems installing the software or packages (ideally before the workshop!).
Submit an issue in the Issue Tracker and we will get back to you as soon as possible.