Add counts per 10k as a normalization option

biolab / orange3-single-cell

🍊🔬 Orange add-on for gene expression of single cell data

https://singlecell.biolab.si/

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Add counts per 10k as a normalization option #395

Closed elapraznik closed 11 months ago

elapraznik commented 1 year ago

Issue

Besides CPM or counts per million, the single-cell literature also mentions CP10K or counts per 10000 as a normalization method. The difference in the method is noticeable after logarithmizing the data and in later downstream analysis.

Description of changes

Added a few lines of code to NormalizeSamples in scpreprocess.py and NormalizeEditor in owspreprocess.py.

Includes

[X] Code changes
[ ] Tests
[ ] Documentation

markotoplak commented 11 months ago

The failing test is unrelated with this PR.