We recently introduced the computation of integration benchmarking metrics (scib-metrics package) to the integration workflow in panpipes. This PR extends the integration tutorial by adding a section describing this additional feature.
Specifically, I did the following:
Added the newly introduced scib parameters to the pipeline.yml file (although I left them empty since we do not have cell type annotation for the data; the scib metrics are calculated irrespective of this).
Added a tutorial section that describes what the scib metrics are, which metrics are calculated under which circumstances, and a preview into actual output data when running the tutorial.
We recently introduced the computation of integration benchmarking metrics (
scib-metricspackage) to the integration workflow in panpipes. This PR extends the integration tutorial by adding a section describing this additional feature.Specifically, I did the following:
pipeline.ymlfile (although I left them empty since we do not have cell type annotation for the data; the scib metrics are calculated irrespective of this).