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Fix link to pre-computed embeddings in paper
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willgryan committed Feb 2, 2024
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Expand Up @@ -54,7 +54,7 @@ PAVER uses vector embeddings to help interpret pathway analyses. Embeddings enco

![PAVER uses numerical representations of pathways to find functionally related clusters.\label{fig:overview}](figures/overview.png)

PAVER was designed to be easy to use by researchers with minimal programming experience. PAVER has already been used in a number of scientific publications to aid in the interpretation of pathway analyses [@william_ryan_2023_8156248; @RN78; @ODonovan_Ali_Deng_Patti_Wang_Eladawi_Imami_2024; @Hu_Sun_Tang_Ryan_Shrestha_Gautam_Lad_Huntley_Haller_Kennedy_2024]. We have pre-computed vector representations for Gene Ontology [@RN68] using the recent anc2vec model [@RN13], available here: https://github.com/willgryan/PAVER_embeddings. However, embeddings for any pathway database or ontology can be used with PAVER.
PAVER was designed to be easy to use by researchers with minimal programming experience. PAVER has already been used in a number of scientific publications to aid in the interpretation of pathway analyses [@william_ryan_2023_8156248; @RN78; @ODonovan_Ali_Deng_Patti_Wang_Eladawi_Imami_2024; @Hu_Sun_Tang_Ryan_Shrestha_Gautam_Lad_Huntley_Haller_Kennedy_2024]. We have pre-computed vector representations for Gene Ontology [@RN68] using the recent anc2vec model [@RN13], available here: [https://github.com/willgryan/PAVER_embeddings](https://github.com/willgryan/PAVER_embeddings). However, embeddings for any pathway database or ontology can be used with PAVER.

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