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How should I assign a pathway/pathways to the target genes when running nichenetr? #267
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Dear user,
Unfortunately, we do not provide enrichment procedures based on target genes or predicted ligands in our package yet. |
Thanks for your reply, active_ligand_target_links_df = best_upstream_ligands %>% lapply(get_weighted_ligand_target_links, geneset = geneset_oi, ligand_target_matrix = ligand_target_matrix, n = 200) %>% bind_rows() %>% drop_na()
active_ligand_target_links = prepare_ligand_target_visualization(ligand_target_df = active_ligand_target_links_df, ligand_target_matrix = ligand_target_matrix, cutoff = 0.33) Moreover, if there is no function for enrichment analysis do you recommend any way to do so out of nichenetr (as you had one case in tutorial that target genes are the genes of a specific pathway)? |
Dear Paria, To perform the analysis, you can use TopGO since it conveniently allows you to adjust for the gene universe. This package also supports enrichment procedures that leverage limitations that could arise if you use hierarchical structured annotations, such as GO-terms (e.g. parent-child terms relationships and information redundancy. Please, refer to Alexa 2006 for more info). I can not help suggesting specific sources for pathway annotations, since their quality might be subjective. Best regards, |
Dear nicheNetR Team,
Following my nichnetr analysis, I have generated a list of target genes and I am interested in assigning pathways to these genes. Could you kindly advise if there is a function available within nicheNetR for pathway enrichment analysis of target genes? I am aware the we are talking about signaling pathway, but for example the neuroglia/ Neurexin signaling pathway could lead to different downstream pathways.
Additionally, I am considering conducting Weighted Gene Co-expression Network Analysis (WGCNA) and would like to integrate this analysis with the findings from nicheNetR. Is there a recommended approach to relate the results of these two analyses for a comprehensive understanding?
Thank you very much for your support and insights.
Best regards,
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