SpotGLM

SpotGLM is an R package for performing cell type-specific differential testing in spatial omics data. It adapts to different data modalities, such as gene expression, chromatin accessibility, or isoform usage, and identifies cell type specific changes associated with local tissue context. SpotGLM accounts for the mixed-cell composition inherent to spatial barcoding technologies.

SpotGLM is integrated with the SPARROW package, making it fast and ultra-scalable for data sets with millions of spots.

Schematic of SpotGLM Analysis

Installation

To install SpotGLM from GitHub:

install.packages("devtools")
devtools::install_github("kaishumason/SpotGLM") # install

We strongly recommend using SpotGLM with SPARROW, which is a power-preserving data reduction method which can speed up analyses. SPARROW can also be installed from GitHUB:

install.packages("devtools")
devtools::install_github("kaishumason/SPARROW") # install

Getting Started

Please follow these tutorials to get started on your data:

Using SpotGLM with SPARROW on Visium HD

Using SpotGLM on Visium data

SpotGLM for isoform switching analysis on spatial long read data

SpotGLM for spatial ATAC analysis

Here is a more technical tutorial that applies spotGLM to simulation data. By working with simulation data, you can see the generative model used in spotGLM:

Demonstration of SpotGLM on simulation data