While GenePattern offers a platform for running PTM-SEA, we don't actually develop it.
I'd recommend reaching out to the authors of PTM-SEA. You might open a ticket at their GitHub repository https://github.com/broadinstitute/ssGSEA2.0.
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego
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