Jean Fan

Dear Matias, Yes you heard correctly! Please check out our various tutorials including those working with Visium 10XGenomics public datasets here: https://jef.works/MERINGUE/ Hope that helps, Jean

Dear Jihyun, Thanks for reaching out. There is a `spatialCrossCorTest` function available that will use permutation testing to provide p-values. Here is a tutorial with more examples for your reference:...

Dear Dmytro, Thanks for reaching out. Does running `setGexpMats` provide you with any other message when `verbose=TRUE`? Without seeing a snippet or knowing the dimensions of your `cancer_matrix` and `ref_matrix`,...

VisCello Shiny App: https://github.com/qinzhu/VisCello

- [ ] Stream in big csv file instead of loading it all (will become more important later as files get so big that they would crash the browser) https://www.papaparse.com/demo

- [x] Allow numeric / non-categorical data to be reflected in opacity (accommodate column for quality) - [x] Allow numeric / non-categorical data to be reflected in radius size, shape,...

- [ ] Allow change of background color (black or white) - [ ] Allow multiple coloring modes; allow coloring points by factor (cell-type) or coloring points by continuous variable...

Hi everyone, This blog post and accompanying video walking through a simulation-based approach for exploring why we don't need normalization with STdeconvolve may be useful for you as you explore...

- [x] `fitLDA` plot doesn't render if only one K is provided. Can check if `length(Ks)==1` and make one point if that's the case. ``` ldas

Dear Nick, This tutorial for aligning Visium datasets may be useful to you: https://jef.works/blog/2023/11/05/aligning-visium-using-STalign-with-reticulate/ In general, for aligning two Visium datasets, I would recommend aligning the Cytassist images and then...