Data without gRNA UMI count matrix

[Larrycpan]

A very nice tool! I am dealing with perturbation data without gRNA matrix UMI count matrix (low MOI). Is it correct to manually transform the perturbation status of each cell into a binary gRNA matrix for input of the function import_data? Additionally, is it possible for SCEPTRE to handle high MOI data where gRNA UMI counts are not available? Thanks for you reply.

[ekatsevi]

I will convert this issue to a Discussion and address it there.

[ekatsevi]

We are working on a feature to allow you to input gRNA assignment matrices directly. In the meantime, I recommend you input a binary (i.e. 0/1) perturbation assignment matrix to sceptre and use assign_grnas(method = "thresholding", threshold = 1) to "assign gRNAs". This will have the intended effect. This approach is compatible with both low- and high-MOI data.