Seppe De Winter

Hi @YH-Zheng You are correct about those two metrics, however for plotting them we invert their values (hence the "inv" prefix). I would not run topic modelling separately per cell...

Hi @w1973145618 I fixed this error some days ago, https://github.com/aertslab/pycisTopic/commit/5416709112f7324152591e66474bbc67ac553306 Can you try reinstalling pycisTopic? All the best, Seppe

Hi @w1973145618 Yes that was my bad as well. It should be fixed now: https://github.com/aertslab/pycisTopic/commit/284c5a53cc7e2f2e85b76f68f0612e0c0a98d29a. Can you try reinstalling? All the best, Seppe

Hi @midichlorianrich There seems to be an issue reading the blacklist bed file. Can you try reading it like this to see if you still have the same error? ```python...

Hi @crsky1023 What is your ray version? ```python import ray ray.__version__ ``` Does the following code produce the same error? ```python import ray ray.init() ray.shutdown() ``` If not, does this...

Hi @etiennedanis Seems to be an issue related to pyranges. What is the version of your pyranges? For me it worked with version 0.0.127. Best, Seppe

Hi @mossconfuse Can you send me an e-mail to [email protected]. I will send you a link to the loom file. Could you please share what command you were running when...

Hi @jklvrt Which versions of umap and pynndescent do you have? ```python import umap import pynndescent umap.__version__ pynndescent.__version__ ``` Maybe updating to the latest version will fix your issue? Best,...

Hi @Meiyuhaha This seems to be an incompatibility between pandas and pyranges. What versions do you have for both packages? Best, Seppe

Hi @Meiyuhaha Is this the full error log? Could you please post the full log, I'm not able to see where things go wrong here. Best, Seppe