Question about score_all_cells and hubs

[kiwipeel]

Hi ,

I am working on only T cells , I was wondering should I use score_all_cells functions by subsetting my data into both condition and samples like this :

adata.obs['T cell_therapy'] = sp.score_all_cells(adata, hubs.hubs[('Lymphoid', 'T cell', 1)],
identifiers = ['condition', 'mice_no'])

I want to make comparison between my two condition afterwards. All samples are collected from same tissue.

And how can I learn general function of hub 1 or hub 2 in T cells?

[mousepixels]

That looks like a reasonable way to do it unless the number of cells per grouping is small (~ <100).

If there is technical batch differences (e.g., depth) between your mice or conditions I would recommend trying binarize = False

I also recommend using a translator just to check there is gene naming concordance.

Please let me know if you have any other questions!

[kiwipeel]

That looks like a reasonable way to do it unless the number of cells per grouping is small (~ <100).

If there is technical batch differences (e.g., depth) between your mice or conditions I would recommend trying binarize = False

I also recommend using a translator just to check there is gene naming concordance.

Please let me know if you have any other questions!

ın the tutorials all cells are scored together , why?

and my other question is this : how can I learn general function of hub 1 or hub 2 in T cells?