Anna Schaar
Anna Schaar
Hi @wangjiawen2013, Thanks for your intest in NCEM. We support 10x visium data that was deconvoluted with a method of your choice. Important step is to export cell type abundances...
Hi @wangjiawen2013, the dataset we used for showing the usecase for Visium data can be loaded and deconvolved as described here: https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html
I generally agree but we aimed to not base our recommendation based on claims from method authors, but only independent benchmarks. Feel free to add one additional sentence, but potentially...
Hi @hai178912522, we are on it! As you can imagine there are more people involved (authors of the chapters, core best practices team, etc.) and I do not have access...
cannot change the GSEA/Pathway data loading to pertpy as it changes results bc of dependency issues
CCC - Then use pertpy -> not working due to dependency issues
deviance feature selection provides a batch parameter, as also noted in the official documentation, https://rdrr.io/bioc/scry/man/devianceFeatureSelection.html I think you have a valid point and generally performing it batch wise should be...
Hi @ErikaZ95, @ngvananh2508 answer is correct, is your question resolved by the answer? and thanks @ngvananh2508!