Steven

Hello @ghuls @SeppeDeWinter I got the same following error by running: from pycisTopic.diff_features import * imputed_acc_obj = impute_accessibility(cistopic_obj, selected_cells=None, selected_regions=None, scale_factor=10**6) normalized_imputed_acc_obj = normalize_scores(imputed_acc_obj, scale_factor=10**4) variable_regions = find_highly_variable_features(normalized_imputed_acc_obj, plot =...

It appears that deleting all other dr_cell files worked, and I was able to retrieve the loom files. However, when I attempted to load them onto the scope, nothing happened.

Hello Seppe, Thank you for your response. I followed your suggestion and loaded the loomfile, but there was still no output. I'm wondering whether the issue could be related to...

Hi @SeppeDeWinter, First of all, Seppe, no worries and thank you so much for all of the wonderful tools and all your help! Hi @degrainger, Could you share with us...

Hi Dave, Thank you so much for this update! I will let you know if it works for me. :) Best, Steven

Hi @SeppeDeWinter, @degrainger, @DmitriiSeverinov, I managed to make it work too! However, I am still confused with some parameters in this function. How do you choose the HVR (highly variable...

Hi @degrainger, Thank you for this advice, it seems to be a good start. I am gonna try this first to see how the results look! I will be happy...

Thank you! I have another problem in the next following step: from scenicplus.wrappers.run_scenicplus import run_scenicplus try: run_scenicplus( scplus_obj = scplus_obj, variable = ['GEX_celltype'], species = 'hsapiens', assembly = 'hg38', tf_file...

Hi Seppe, I've managed to get everything working, but I'm encountering issues with some of the post-analysis steps. It seems that I can't figure out how to plot the old...