Maren Büttner comments

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                                            Maren Büttner

how to calculate the max rejection rate and labeled the line in line chart

Closed as stale.

how to assess the batch? by rejection rate or silhouette?

Closed as completed.

Installing issue with KDEpy

thanks @grst for connecting us. Happy to join forces. I have a comparison of CytoPy and pytometry on my list, but did not find the time to do it, yet.

Installing issue with KDEpy

Hi @burtonrj happy to finally start the discussion and thanks for the flowers 💐 I'll PM you to take the discussion elsewhere. On a different note for @grst, we could...

Improve runtime of kBET

Hi @liliay thank you for trying kBET. 1. I would use the batch label of the cells, not the condition. 2. About the runtime: I recommend to reduce the number...

Improve runtime of kBET

@adamgayoso Thanks for sharing this! Your code looks quite neat and it is fantastic so learn about the speed-up. Did you also include an estimate on the neighborhood size? I...

Using kBET with AnnData object

Closed as no reply.

Adjust Combat for control cells

> Should the reference object where you learn the transformation always be a subset of the data you're going to apply the transformation to? If so, instead of passing a...

interpreting the output with the issue of compositionality.

Hi Marwan, thank you for your questions. 1) We expect more "hits" with a Poisson regression and Wilcoxon rank sum test, because both models ignore the nature of compositional data....

interpreting the output with the issue of compositionality.

Hi @FionaL720 thank you for sharing your issue. I have some questions: Do you have n=5 samples total or per condition? What is the overall abundance of your clusters? How...