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rnabioco / djvdj

An R package to analyze single-cell V(D)J data
https://rnabioco.github.io/djvdj
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Differences in diversity analysis when using other packages #142

Closed abedkurdi closed 1 month ago

abedkurdi commented 4 months ago

Hello there,

First, I would like to thank you for this great package, I have been looking for such tool a while ago! Second, I was comparing the diversity plots, output from your package and output from scRepertoire R/Bioconductor package.

I thought I would be able to reproduce, if not identical results, something very similar when using both packages. However, it was not the case Screenshot from 2024-03-11 14-25-12

Screenshot from 2024-03-11 14-25-51

I counted the number of unique clonotypes in both analyses and I got the exact same number for each hashtag.

Do you have any idea what could be happening here? I appreciate your help.

sheridar commented 1 month ago

Hi @abedkurdi, sorry about the delay, I'm looking into this

abedkurdi commented 1 month ago

Hello @sheridar The reason behind this is bootstrapping.

sheridar commented 1 month ago

This issue seems resolved, feel free to open a new issue if you have any other issues/questions