Closed Hego-CCTB closed 7 months ago
Done here: 9a63d9dfd7cb9e30db31a8d341adceea6bab73c7
--skip_curation yes
stops curate
after the transformation of the count table and the curate_group.mean version of that table and before any kind of batch-effect removal/outlier removal/mapping-rate cut-off.
--skip_curation no
behaves normally (default. https://github.com/kfuku52/amalgkit/commit/22e34c6d2779138bb7729d37e300a89fab9b54a9).
Thank you. Could you bump the version?
done
We recently encountered a case, where samples were (intentionally) extremely similar to each other, despite being tagged as different tissues. This led to amalgkit removing a couple of samples. Additionaly for that dataset, we didn't need the amalgkit corrected output at all. So it would be nice to have an option to just output all data before the SVA correction and then stop, saving some time in cases where SVA correction is not desired.