Package index • SVG

Package Overview

Package-level documentation

SVG SVG-package: SVG: Spatially Variable Genes Detection Methods for Spatial Transcriptomics

Unified Interface

Main entry point for SVG detection

CalSVG(): Unified Interface for SVG Detection

SVG Detection Methods

Individual SVG detection method implementations

CalSVG_MERINGUE(): MERINGUE: Moran's I based Spatially Variable Gene Detection

CalSVG_binSpect(): binSpect: Binary Spatial Enrichment Test for SVG Detection

CalSVG_SPARKX(): SPARK-X: Non-parametric Kernel-based SVG Detection

CalSVG_Seurat(): Seurat-style SVG Detection Methods

CalSVG_nnSVG(): nnSVG: Nearest-Neighbor Gaussian Process SVG Detection

CalSVG_MarkVario(): Detect SVGs using Mark Variogram Method

Spatial Network Utilities

Functions for building spatial neighborhood networks

utils_spatial: Spatial Network Utilities

buildSpatialNetwork(): Build Spatial Neighborhood Network

getSpatialNeighbors_Delaunay(): Build Spatial Network via Delaunay Triangulation

getSpatialNeighbors_KNN(): Build Spatial Network via K-Nearest Neighbors

adj_to_edgelist(): Convert Adjacency Matrix to Edge List

row_standardize(): Row Standardize Adjacency Matrix

Statistical Utilities

Statistical functions used by SVG methods

utils_stats: Statistical Utilities for SVG Detection

moranI(): Calculate Moran's I Statistic

moranI_test(): Moran's I Test for Spatial Autocorrelation

ACAT_combine(): ACAT: Aggregated Cauchy Association Test

binarize_expression(): Binarize Gene Expression

davies_pvalue(): Davies' Method for Quadratic Form P-values

liu_pvalue(): Liu's Method for Approximating P-values

lisa_test(): Local Indicators of Spatial Association (LISA)

Data Simulation

Functions for generating simulated spatial data

data_simulation: Simulate Spatial Transcriptomics Data with Known SVGs

simulate_spatial_data(): Simulate Spatial Transcriptomics Data

generate_spatial_pattern(): Generate Spatial Expression Pattern

generate_hexagonal_grid(): Generate Hexagonal Grid Coordinates

generate_square_grid(): Generate Square Grid Coordinates

generate_random_coords(): Generate Random Coordinates

Example Data

Built-in example datasets

example_svg_data: Example Spatial Transcriptomics Data

C++ Accelerated Functions

High-performance C++ implementations

moranI_cpp(): Fast Row-wise Moran's I Calculation

moranI_full_cpp(): Fast Moran's I with Full Statistics

binarize_kmeans_cpp(): Fast Binarization using K-means (k=2)

dist_matrix_cpp(): Fast Distance Matrix Computation

knn_adj_cpp(): Build KNN Adjacency Matrix

fisher_spatial_cpp(): Compute Fisher's Exact Test for Spatial Enrichment