Python API Reference

gesso (Gene sEt activity Score analysis with Spatial lOcation) is a Python package designed for the analysis of spatial transcriptomics expression data at the gene set/pathway level. Given a user-provided gene set/pathway, gesso computes a gene set activity score (GAS) for each spatial spot in the dataset.

• GESSO (gesso.GESSO)
  • GESSO
    • GESSO.__init__()
    • GESSO.compute_gas()
    • GESSO.htest_elevated_gas()
• GeneSetActivityScoresReport (gesso.GeneSetActivityScoresReport)
  • GeneSetActivityScoresReport
    • GeneSetActivityScoresReport.gas_df()
    • GeneSetActivityScoresReport.gene_contributions_df()
    • GeneSetActivityScoresReport.locations_df()
    • GeneSetActivityScoresReport.plot_gas_spatial_map()
• PermutationTestReport (gesso.PermutationTestReport)
  • PermutationTestReport
    • PermutationTestReport.gas_df()
    • PermutationTestReport.htest_df()
    • PermutationTestReport.locations_df()
    • PermutationTestReport.plot_gas_spatial_map()
    • PermutationTestReport.plot_pval_spatial_map()
    • PermutationTestReport.pval_df()