Running multinichenet for a single sampleID but 3 groupID

[ceciih]

Running multinichenet for a single sampleID but 3 groupID

[browaeysrobin]

Hi @ceciih

The error message that is thrown in case you want to analyze 1 sample/patient is a "feature not a bug" since it is not possible to perform proper DE analysis with the pseudobulk-edgeR framework in that case.

In general, we strongly recommend having at least 4 samples in each of the groups/conditions you want to compare.

However, we also understand that it's sometimes not possible to reach this number of samples for analyses, and that you still want to explore cell-cell communication patterns in your data.
For these instances, we have developed a new "sample-agnostic" workflow to perform differential cell-cell communication with a MultiNicheNet-like prioritization framework : Differential cell-cell Communication for datasets with limited samples: “sample-agnostic/cell-level” MultiNicheNet.

(note, running this vignette requires updating to multinichentr 2.0.0)