From befe797a49a72ee11668ce29da30142bc73a6643 Mon Sep 17 00:00:00 2001 From: William Ryan Date: Fri, 2 Feb 2024 00:42:26 -0500 Subject: [PATCH] Fix link to pre-computed embeddings in paper --- joss/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/joss/paper.md b/joss/paper.md index 754be58..7e81d3b 100644 --- a/joss/paper.md +++ b/joss/paper.md @@ -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. # Licensing, Availability and Usage