CBW Workshop R Notebooks
1
Index
2
CBW Workshop example R Notebooks
3
Setup
3.1
Install R and RStudio
3.2
Docker [Optional]
3.3
Install Docker
3.3.1
Windows
3.3.2
MacOS / Linux
4
Run g:profiler from R
4.1
Initialize variables and libraries
4.2
Load in Query set
4.3
Run g:profiler with supplied genesets
4.4
Download and load g:profiler geneset file
4.5
Filter results by geneset size
4.6
Create an output file of the results - Generic enrichment Map file from g:profiler gmt
4.7
Run g:profiler with your own genesets (example using BaderLab genesets)
4.8
Download and load Bader lab geneset file
4.9
Filter Bader lab geneset file
4.10
Upload the gmt files to gprofiler
4.11
Create an output file of the results - Generic enrichment Map file from Baderlab gmt
5
Run GSEA from within R
5.1
Load in required libraries
5.2
Configurable Parameters
5.3
Download the latest pathway definition file
5.4
Run GSEA
6
Create GMT file from Ensembl
6.1
Load Libraries
6.2
Set up Biomart connection
6.3
Get species GO annotations
6.4
Format results into GMT file
7
Translate human gmt file to another species using ensembl
7.1
Load in required libraries
7.2
Download the latest pathway definition file
7.3
Set up Biomart connection
7.4
Convert the species genes from human
7.5
Format results into GMT file
8
Create Enrichment map from R with g:Profiler results
8.1
Initialize variables and libraries
8.2
Configurable Parameters
8.3
Specify Data files
8.4
Launch Cytoscape
8.5
Make sure you can connect to Cytoscape
8.6
Create an Enrichment map
8.7
Create an Enrichment map - run EM command
8.8
Get a screen shot of the initial network.
9
Create Enrichment map from R with GSEA results
9.1
Initialize variables and libraries
9.2
Configurable Parameters
9.3
Specify Data files
9.4
Optional File specification
9.5
Launch Cytoscape
9.6
Make sure you can connect to Cytoscape
9.7
Create an Enrichment map
9.8
Create an Enrichment map - run EM command
9.9
Get a screen shot of the initial network.
10
References
Bader Lab
Translate gmt file from human to another species
Translate gmt file from human to another species
Ruth Isserlin
2024-06-19
Chapter 1
Index
