Function reference • DiCoLo

Compute Gene-gene Optimal Transport Distance
`SelectCommonGenes()`	Select common variable genes across two Seurat objects
`ComputeGeneEMD()`	Compute gene Earth Mover's Distances via a Python backend
`LoadGeneEMD()`	Load a gene EMD distance matrix from disk
Construct Gene Graphs
`ComputeGraphOperator()`	Compute a positive semi-definite gene graph operator
`ComputeDifferentialOperator()`	Compute the differential co-localization operator
Select Significant Genes & Gene Modules
`FindKneePoint()`	Find the knee point of an eigenvalue curve
`SelectSignificantGenes()`	Select significant genes per eigenvector using local FDR
`ClusterGenes()`	Cluster genes using hierarchical clustering and dynamic tree cutting
`RankGeneModules()`	Rank gene modules by eigenvector importance
Visualization
`ObtainGeneTSNE()`	Compute a 2-D t-SNE embedding of genes from a distance matrix
`VisualizeGeneTSNE()`	Visualise a gene t-SNE coloured by module or continuous score
Other
`RunSVD()`	Run a truncated symmetric eigendecomposition

Reference