Haojia Wu

@tsvvas Thanks for your interest in our package. We have not tested on Julia v1.9.3. Maybe there are some dependency issues. I am using Julia V1.7.3 currently. I also tested...

I will test it on a newer version of Julia later. The issues you came across are most likely the dependencies compatibility issue. That happened to me when I used...

Hi @tsvvas @MaximilianNuber , I made a new branch for Julia 1.9 to fix the dependency issue. Please re-install the package using the commands below: ```Julia using Pkg Pkg.add(url="https://github.com/bicycle1885/Leiden.jl") Pkg.add(url="https://github.com/HaojiaWu/CellScopes.jl#julia_v1_9")...

Hi @Pedro-Pei Thanks for your interest in using CellScopes. Unfortunately we have not tested CellScopes on a personal MacBook since the computing power of a MacBook is usually not enough...

Hi @ayumatsubo Thanks for your interest in trying CellScopes. Yes, this is on our to-do list. It will be available soon. Stay tuned!

"1. Is there anyway to save CellScopes figures from the julia command line as a pdf or svg for instance?" **yes, try this:** ```julia ]add CairoMakie import CairoMakie as MK...

Thank you for your interest in CellScopes. To use the ```from_seurat``` function, there are two prerequisites: 1. Your Seurat object needs to be fully processed. This includes completing cell clustering...

I fixed it. Now CellScopes supports Seurat V5. You may need to reinstall the package. ```julia using Pkg; Pkg.rm("CellScopes") Pkg.add(url="https://github.com/bicycle1885/Leiden.jl") Pkg.add(url="https://github.com/HaojiaWu/CellScopes.jl") import CellScopes as cs seurat_sc = cs.from_seurat("pbmc3k.rds"; data_type="scRNA", assay="RNA",...

I see. Your object is from Visium, not regular scRNA. I haven't tested Visium since upgrading this function to accommodate Seurat V5. I will take a look and let you...

@YuxiZhang-0113 @Emily-Stranger It should work for the rds file prepared by Seurat V5 now. For scRNA-seq: ``` seurat_sc = cs.from_seurat("rna_test_sct.rds"; data_type="scRNA", assay="SCT") ## or if you prepared the object from...