I have done an analysis using scanpy and related sc-verse pipelines of a large number of separate data sets (8). These represent three different time points and for each time point I have two conditions. I would like to integrate this data, and personally found the seurat integration pipeline to be best for doing this. However, as far as I know there is no python equivalent of this anchor-based integration approach, am I right? Do you have other suggestions for how to integrate the data using a python-based method?
Hi, I have a very similar question. I am handling a number of cell ranger output files from different experiments and integrating them to together.
I think Integration is just reading all the files in a for loop and concatenating them. But the issue I am having is adding metadata of the experiments? like type of organ, etc? Is there a way to add those
I think this question is a bit different, since it’s not about accounting for batch effects in the data. I’ve addressed this in your other post here: