Handling replicates from same time point

beiko-lab / ananke

Ananke: Clustering marker gene data by time-series patterns

MIT License

9 stars 2 forks source link

Handling replicates from same time point #3

Open elsherbini opened 6 years ago

elsherbini commented 6 years ago

Does ananke handle replicates from the same time point? From reading calculate_slopes in _cluster.py it looks like it would see replicates as an issue. Would it be possible to add an option for computing the mean of samples for each time point and then proceeding?

elsherbini commented 6 years ago

As a follow up, is it appropriate to simply take the mean of the counts of each ASV for each time point? Will zero imputation and CLR transformation proceed with non-integer "counts"?