Giovanni Palla comments

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                                            Giovanni Palla

error loading Nanosctring CosMx dataset

hi @GhobrialMoheb unfortunately I am not able to help with this error message, can you try to create the anndata from the various files instead of reading it with the...

Comparisons between groups of samples

@Zethson we discussed this before going on holiday, we have a zulip channel for that, I'll add you

Add method to calculate embeddings for variable by distance aggregation

hi @LLehner , thank you for this, would you mind elaborating a bit when this would be used? also, what if the embedding are pre-calculated, or the user would like...

Reading in MERSCOPE sample data with squidpy.read.vizgen() doesn't work for every dataset?

hi @Laura-Waechter , could you try to install form main? `pip install git+https://github.com/scverse/squidpy@main` let me know if it works,

Reading in MERSCOPE sample data with squidpy.read.vizgen() doesn't work for every dataset?

can you try with #679 ?

Reading in MERSCOPE sample data with squidpy.read.vizgen() doesn't work for every dataset?

it is in main, thank you again @dfhannum . Am trying to cut release asap but encountering few hiccups, but should manage to do it this week.

Reading in MERSCOPE sample data with squidpy.read.vizgen() doesn't work for every dataset?

hi both, I think the version in conda is not up to date yet, so please use the pip installable version

Bug about sq.im.ImageContainer() function in WSL2-VScode

hi @yunbokai unforutnately I have no clue and don't have capacity to test with WSL, not sure if you found a solution already?

sq.gr.co_occurrence gives different results for n_splits=1 and n_splits>1

yes, it's expected, that is because of the way the co-occurrence is implemented, we split the data in chunks if it is too large. I would suggest to split the...

Cannot load Visium_FFPE_Mouse_Brain,Visium_FFPE_Human_Normal_Prostate. Error: HTTP Error 403: Forbidden

we should probably deprecate the datasets module, since it seems that the API requests have often issues, and also that there are many more datasets, that can't be directly read...