He, Peng 何鹏

> @SamAllon running homebrew as root in configure file is no longer supported for obvious safety reasons. > > Just open terminal and run the part yourself (assuming you have...

The Cluster 5 only has 1 cell there. There are more doublets contributed by Cluster 5 though.

This issue has appeared in Cufflinks, too. Our lab solves this problem by setting --max-bundle-length 4500000 so that it exceeds the largest transcript size in ENSEMBL gtf file. But we...

I'm not sure which part of your codes need modification. Could you add some comments into the codes to make sure I understand how they work? I then can integrate...

This can be very useful! It's becoming increasingly popular to see 3D UMAPs! [Cao et al 2020](https://science.sciencemag.org/content/370/6518/eaba7721/tab-figures-data) 's Figure 1 used it. Discussions about 3D embeddings had been there as...

Actually I just realized that plotly can already visualize 3D scatterplots nicely. But it can't conveniently show gene expressions easily.

> @brianpenghe I'd be excited to see someone hack this in on a fork and experiment! We're already in webgl land, so it's possible in the present architecture. Selections in...

> @brianpenghe I will pass on here that we have seen users who are using a spatial coords in the embedding use coloring by categorical metadata to highlight various structures....

@ambrosejcarr I've been able to use cellxgene's many useful functions. The only inconvenient part now is that I have to open an H&E + Visium spots image, and put it...

Wow this is exactly what we need!!! Because 10X loupe browser can't display cell type signature scores (continuous score). Cellxgene would be the only way we can share our data...