curated_genes |
Curated Genes for example purposes |
find_genes_of_interest |
find_genes_of_interest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes. |
getInteractingGenes |
getInteractingGenes Calculate Interaction Regions and Associated Genes This function calculates statistically significant genes using a non-parametric Kruskal-Wallis test for genes in any one region of influence and a post hoc Dunn's test is used for analysis of genes between regions. |
getPairwiseInteractingGenes |
getPairwiseInteractingGenes |
getSpatialFeatures |
getSpatialFeatures Load spatial features |
getSpatialParameters |
getSpatialParameters Calculate the Optimal Parameters for Interacting Cells |
getSpatialParametersExternal |
getSpatialParametersExternal Manually obtain Optimal Parameters for Interacting cells |
load10XCoords |
load10XCoords Load 10x Visium Spatial Coordinates |
load10XExpr |
load10XExpr load 10X Visium Expression Data |
optParams |
Optimal paramters of 5 patterns from CoGAPS. |