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SVG: Spatially Variable Genes Detection Methods

A unified R package for detecting spatially variable genes (SVGs) in spatial transcriptomics data, integrating multiple state-of-the-art methods with optimized performance.

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Version

Install

install.packages('SVG')

Version

1.0.0

License

MIT + file LICENSE

Issues

0

Pull Requests

0

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0

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0

Maintainer

Zaoqu Liu

Last Published

February 1st, 2026

Functions in SVG (1.0.0)

generate_square_grid

Generate Square Grid Coordinates
getSpatialNeighbors_Delaunay

Build Spatial Network via Delaunay Triangulation
binarize_expression

Binarize Gene Expression
moranI_full_cpp

Fast Moran's I with Full Statistics
row_standardize

Row Standardize Adjacency Matrix
simulate_spatial_data

Simulate Spatial Transcriptomics Data
utils_spatial

Spatial Network Utilities
utils_stats

Statistical Utilities for SVG Detection
getSpatialNeighbors_KNN

Build Spatial Network via K-Nearest Neighbors
dist_matrix_cpp

Fast Distance Matrix Computation
knn_adj_cpp

Build KNN Adjacency Matrix
binarize_kmeans_cpp

Fast Binarization using K-means (k=2)
davies_pvalue

Davies' Method for Quadratic Form P-values
buildSpatialNetwork

Build Spatial Neighborhood Network
generate_spatial_pattern

Generate Spatial Expression Pattern
moranI_test

Moran's I Test for Spatial Autocorrelation
generate_random_coords

Generate Random Coordinates
data_simulation

Simulate Spatial Transcriptomics Data with Known SVGs
moranI

Calculate Moran's I Statistic
zzz

Package Startup Messages
moranI_cpp

Fast Row-wise Moran's I Calculation
CalSVG_Seurat

Seurat-style SVG Detection Methods
ACAT_combine

ACAT: Aggregated Cauchy Association Test
CalSVG_MERINGUE

MERINGUE: Moran's I based Spatially Variable Gene Detection
CalSVG_MarkVario

Detect SVGs using Mark Variogram Method
CalSVG_nnSVG

nnSVG: Nearest-Neighbor Gaussian Process SVG Detection
CalSVG_binSpect

binSpect: Binary Spatial Enrichment Test for SVG Detection
SVG-package

SVG: Spatially Variable Genes Detection Methods for Spatial Transcriptomics
CalSVG

Unified Interface for SVG Detection
CalSVG_SPARKX

SPARK-X: Non-parametric Kernel-based SVG Detection
fisher_spatial_cpp

Compute Fisher's Exact Test for Spatial Enrichment
adj_to_edgelist

Convert Adjacency Matrix to Edge List
generate_hexagonal_grid

Generate Hexagonal Grid Coordinates
example_svg_data

Example Spatial Transcriptomics Data
.check_cpp

Check if C++ Functions are Available
lisa_test

Local Indicators of Spatial Association (LISA)
liu_pvalue

Liu's Method for Approximating P-values