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Copy file name to clipboardExpand all lines: README.md
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Rust implementation of [WebGestaltR](https://github.com/bzhanglab/webgestaltr).
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## Notes
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This CLI is focused purely on computation. **It does not provide GMT files or HTML reports**. The output of this tool is JSON files containing the results. For a more feature-complete tool, see the original [WebGestaltR](https://bzhanglab.github.io/WebGestaltR/) tool.
Example of running over-representation analysis using `kegg.gmt`, with an interesting list at `int.txt` and a reference of `ref.txt`. Outputs JSON file at `output.json`
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```shell
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ora -g kegg.gmt -i int.txt -r ref.txt -o output.json
Copy file name to clipboardExpand all lines: webgestalt_lib/src/methods/multilist.rs
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/// # Parameters
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///
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/// - `jobs` - A [`Vec<GSEAJob>`] containing all of the separates 'jobs' or analysis to combine
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/// - `method` - A [`MultiOmicsMethod`] enum detailing the analysis method to combine the runs together (meta-analysis, mean median ration, or max median ratio).
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/// - `method` - A [`MultiListMethod`] enum detailing the analysis method to combine the runs together (meta-analysis, mean median ration, or max median ratio).
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/// - `fdr_method` - [`AdjustmentMethod`] of what FDR method to use to adjust p-values
/// Uses random walk to calculate the neighborhood of a set of nodes
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/// Returns [`Vec<String>`]representing the nodes in the neighborhood
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/// Uses random walk to calculate the probabilities of each node being walked through
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/// Returns [`Vec<String>`] representing the nodes in the neighborhood
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///
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/// ## Parameters
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/// - `config` - A [`NTAConfig`] struct containing the edge list, seeds, neighborhood size, reset probability, and tolerance
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///
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/// # Parameters
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/// - `config` - A [`NTAOptions`] struct containing the edge list, seeds, neighborhood size, reset probability, and tolerance
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pubfnnta(config:NTAConfig) -> Vec<(String,f64)>{
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/// ## Returns
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///
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/// Returns a [`Vec<(String, f64)>`] where the [`String`] is the original node name, and the following value is the random walk probability (higher is typically better)
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