SpatialPath

SpatialPath is a pipeline that provides pathway-level activity scores across spatial omics datasets. The goal of SpatialPath is to process your data so that you can get to the fun part of the analysis quicker.

The workflow for SpatialPath is shown below. Inputs include FASTQ's, along with histology images, which are put through numerous analyses including read mapping, gene expression quantification, spatial binning and pathway activity scoring. Outputs include spatial plots with pathway level scores overlayed across each sample.

Installation

To set up the SpatialPath environment and download the necessary reference files, run the installation script.

Prerequisites

• Conda installed
• git

git clone https://github.com/cathalgking/SpatialPath.git
cd SpatialPath
./install_spatialpath.sh

Usage

./spatialpath.sh -t 28 -i /path/to/spaceranger/output -s mouse -p /path/to/spatialpath

Command-Line Options

• -t <threads>: Number of threads to use (default: 1)
• -i <input_folder>: Input folder (must be the output from Spaceranger)
• -s <species>: Species (mouse or human)
• -p <spatialpath_dir>: Location of SpatialPath installation