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benfulcher committed Jun 30, 2020
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## Preparation: Defining gene-to-category annotations

The first step in running an enrichment analysis is defining the set of gene categories, and the genes annotated to each category.
Results of this, using hiearchy-propagated gene-to-category annotations corresponding to GO biological processes (processed as of 2019-04-17), can be downloaded from [this figshare repository](https://figshare.com/s/71fe1d9b2386ec05f421).
Results of this, using hierarchy-propagated gene-to-category annotations corresponding to GO biological processes (processed as of 2019-04-17), can be downloaded from [this figshare repository](https://figshare.com/s/71fe1d9b2386ec05f421).

Code in this repository also allows you to reprocess these annotations from raw data from GO, as described on [this wiki page](https://github.com/benfulcher/GeneSetEnrichmentAnalysis/wiki/Defining-gene-to-category-annotations).

## Performing Enrichment

### Setting Parameters
All parameter settings for enrichment are kept in a Matlab structure that can be set to defaults as:
```matlab
enrichmentParams = GiveMeDefaultEnrichmentParams();
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