R: Spatial Component Analysis for Spatial Sequencing Data

# Spatial Component Analysis for Spatial Sequencing Data

## Documentation for package ‘SPACO’ version 1.0.2

- DESCRIPTION file.

## Help Pages

create_SpaCoObject_from_KNN | create_SpaCoObject_from_KNN
denoised_projection_plot | Plot denoised gene expression
denoise_profiles | computes smoothed gene profiles of genes present in the data.
eigenMapMatMult | Multiply two matrices using Eigen library
feature_plot | Plot gene expression
read_10x_for_spaco | Read in 10x Visium spatial transcriptomics data
set_projection | Set projections of Spaco Object
seurat_to_spaco | Wrapper to transform existing Seurat object into an SpaCoObject.
SpaCo | SpaCo
SpaCoObject | Create a constructor function that creates an object of class SpaCoObject
Spaco_plot | Plot SPaCo meta genes.
spacs_to_seurat | transfer computed spatial components to existing Seurat object.
subset_non_neighbour_cells | Filtering function to remove cells without neighbours in defined distance from existing Seurat object to be conformable with existing SpaCoObject.
SVGTest | Compute the spatial variable genes of a SpaCoObject after runinng runSCA