spatialtis_core.spatial_de

Subpackages

• spatialtis_core.spatial_de.somde
  • spatialtis_core.spatial_de.somde.som
  • spatialtis_core.spatial_de.somde.util

Submodules

• spatialtis_core.spatial_de.som_de

Package Contents

spatialtis_core.spatial_de.somde(exp: pandas.DataFrame, coord: Union[List, numpy.ndarray], k: int = 20, alpha: float = 0.5, epoch: int = 100, pval: float = 0.05, qval: float = 0.05) → numpy.ndarray

A wrapper for somde, a method to identify spatial variable genes

Publications

Github: SOMDE

Parameters

• exp – A dataframe, gene name as index, spatial points as columns

• coord – N*2 array of coordination

• k – Number of SOM nodes

• alpha – Parameters for generate pseudo gene expression

• epoch – Number of epoch

• qval – Threshold for pval

• pval – Threshold for pval