Immanuel Abdi comments

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                                            Immanuel Abdi

Problem running with Visium HD spatial Data

Hi salasd, Good to see that you're trying to incorporate BPCells into your workflow! From what I see, this is an issue with Seurat rather than BPCells. It would be...

[cpp] Fix matrix Windows/linux matrix compatibility issues

Good catch on the git issues. I didn't know that git automatically changes line return when pulling, and was probably missed because I was only developing on one system. Otherwise,...

SOLUTION: addGeneExpressionMatrix / import10xFeatureMatrix issue

Thanks Julia, I'll add these notes to the to-do list.

Error when using addClusters() on multiome data

Will have this implemented, thanks!

Error when using addClusters() on multiome data

Fixed in dev branch!

Installation

hi @antoine4ucsd , I don't think a lot of our dependencies support the m3/m4 arm chips for R. If you install R using x86/x64 support on version 4.4, bioconductor 3.19,...

matrix with no cells

I'll look into this! Busy until next Tuesday but I'll update you around then. Thanks Brent @brgew

[r] add iterative lsi design docs

`select_features` is good! For your second point comment point, I think my interpretation from that conversation was that the clustering would be separate, but we would still pseudobulk within funciton....

BPCells requires hdf5 (>= 1.12.0)

Good catch, I definitely encountered this before, without thinking to fix it. I'll do so within next few days

BPCells requires hdf5 (>= 1.12.0)

So I've noticed that I can't consistently get version 1.10.5, or version 1.10.10 to fail. Moreover, our CI pipelines actually use v1.10 for hdf5, so I don't think its a...