A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

<@UNCU4LKJM> / others - are you still keen on getting this done? <https://github.com/MultiQC/MultiQC/issues/3348>

Just taking a look at it ahead of the v1.35 release. Wondering a bit if it should go into MultiQC or into the xenium-extra plugin.

<https://github.com/MultiQC/MultiQC/issues/3348#issuecomment-4419304773>

hi <@UE4L64T4G> there is value in adding nuclei per cell metric to Xenium QC as it immediately flags issues with segmentation. It could go to xenium-extra plugin as it requires more extractions than simple cell metrics csv. Is there anything I can help you with?

Sure, sounds good! Please open an issue here: <https://github.com/MultiQC/xenium-extra>

and if you fancy it, a PR :slightly_smiling_face:

<@UE4L64T4G> I have created a PR with this feature: <https://github.com/MultiQC/xenium-extra/pull/4>

<@UE4L64T4G> I want to tackle the other bug I found in the same PR if that's ok? Briefly: on single-sample Xenium reports, the plugin silently skips four cell-related density sections:
```xenium_extra | Skipping cell area density plot - using pre-calculated statistics. Density plots require raw data.
  xenium_extra | Skipping nucleus RNA fraction density plot - using pre-calculated statistics. Density plots require raw data.
  xenium_extra | Skipping nucleus-to-cell area ratio density plot - using pre-calculated statistics. Density plots require raw data.
  xenium_extra | Skipping density plot for transcripts per cell - using pre-calculated statistics. Density plots require raw data.```

Let me know when everything is done and I can review

<https://github.com/MultiQC/xenium-extra/pull/4/changes/b210e7e2efd35048d2559ce5268b70e67ae5e4ad>

you can review, I have tested on 1 sample and see all the missing figures now.