Suoqin Jin

@superman2412 You can check this package https://github.com/jlmelville/uwot and replace the umap function using the function from this package.

@RajneeshSrivastava Do you run umap using 'uwot' or the other one ? Do you have the same umap for each run?

@RajneeshSrivastava Can you run the default method when running netEmbedding, i.e., `"umap-learn"`?

@JKarmanAbbVie Does this result from `netVisual_bubble(cellchat_gse136831_ipf_trimean, sources.use = 'Macrophage', targets.use = 'Myofibroblast', thresh = 1e-300)` look good? I feel there may be a bug when you specifying a signaling.

@bayankizil You can check the tutorial and there is one part we combine the differential expression analysis. The rankNet function also implement a statistical test by setting 'do.stat = TRUE'.

@YitengDang This was an interesting issue. I reinstalled the package from my github, but I did not find any issue. However, you are not the first people mentioned this issue...

@YitengDang @ColeKeenum Can you guys share your cellchat object so that I can replicate the error?

@sofiapuvogelvittini It is so sad to know that this issue has not been well addressed. I am wondering if you would like to share your cellchat object with me and...

@AIYang1210 I suggest you to set `future::plan("multisession", workers = 1)` when running this function. We will fix it when finding a good solution

@Magetutor Your data have negative values. You should use the normalized data without negative values.