How to analyze multiple samples together as integrated/merged?
Yes, it absolutely is!
All samples that you would like to integrate and visualize together should be uploaded to a single project within the Data Management module. For example, in the screenshot below you can see that there are 4 samples in this project that I would like to be integrated together:
Then, in step 6 of the Data Processing module, you can control the integration settings. Note that Cellenics uses the Harmony method of integration by default, but you can choose another method (Seurat or FastMNN) or indeed to not integrate the data at all (select ‘no integration’). We find that Harmony integration works well for the vast majority of datasets.
In this step (step 6), you should ensure that your multi-sample dataset is well integrated. You can use the embedding plot and frequency plot views to ensure that all samples are distributed across all clusters. For example, the screenshot below shows a well-integrated dataset using the Harmony method: