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13-webgestaltr.Rmd
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13-webgestaltr.Rmd
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# WebGestaltR
`WebGestaltR` is the R version of the web application [WebGestalt](www.webgestalt.org), "WEB-based GEne SeT AnaLysis Toolkit".
This tool (both the web and R versions) has many features and advantages:
- Simple to run
- Runs ORA, GSEA, and NTA (network topology analysis)
- Natively supports 12 organisms
- Can be used for novel species (we will do this in the final session)
- Supports many namespaces (n = 73 for human)
- Does not require namespace conversion between the databases like `clusterProfiler` does (it converts to Entrez behind the scenes), and even allows different namespaces between query gene list and ORA background gene list
- Supports many databases/gene sets (n = 70 for human) including 'nonredundant' versions of GO
- Supports metabolomics, with 15 different ID types, described in [Elizarraras et al 2024](https://academic.oup.com/nar/article/52/W1/W415/7684598)
- Can run query against multiple databases simultaneously by providing database names as a list to the enrichment function
- Has term redundancy filters including 3 custom non-redundant GO databases and two clustering algorithms
- Saves all results files to disk when running, no need to save individual files manually
- Creates interactive HTML reports with various plots and filter options and with term links to external databases
- Supports multi-threading, parallelisation, and batch processing of multiple queries
## Activity overview
1. Explore the organisms, databases/gene sets and namespaces supported natively
2. Run ORA over pathway databases and explore the interactive HTML output
3. Run GSEA over the `WebGestalt` `GO noRedundant` and full database and compare the results
<p> </p> <!-- insert blank line -->
➤ Go back to your RStudio interface and clear your environment by selecting `Session` → `Quit session` → `Dont save` → `Start new session`
➤ Open the `WebGestaltR.Rmd` notebook by clicking on it in the `Files` pane
You could also open the file by selecting `File` → `Open file`, or use the keyboard shortcut `ctrl + o`.
**<span style="color: #006400;">Instructions for the analysis will continue from the R notebook.</span>**
<p> </p> <!-- insert blank line -->
## End of activity summary
- We have reviewed the organisms and databases that are natively supported by this easy to use tool
- We have run both ORA and GSEA and explored the interactive HTML results summary
- We have touched on the redundancy filters available within this tool, for GO as well as two external algorithms applied automatically to any enrichment performed
- In the next session, we will use `WebGestaltR` for novel species FEA