GPS: Genetics-informed Pathogenic Spatial Mapping Program

Overview

GPS (Genetics-informed Pathogenic Spatial Mapping) is Python command-line tool designed for ....

Features

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Installation

install use pip:

pip install GPS-mapping

install from source:

git clone
cd GPS-mapping
pip install -e .

Usage

To use GPS, navigate to the command line and enter GPS followed by the subcommand that corresponds to the desired operation. Each subcommand may require specific arguments to run.

Basic Command Structure

GPS subcommand [arguments...]

• subcommand: The specific operation you wish to perform.
• arguments: The arguments and options required for the subcommand.

Available Subcommands

(Provide a list and brief description of each available subcommand. For example:)

• run_find_latent_representations: Finds latent representations using a GNN-VAE model.
• run_latent_to_gene: Maps latent representations to gene markers.
• run_generate_ldscore: Generates LD scores for genomic spots.
• run_spatial_ldsc: Conducts spatial LDSC analysis.
• run_cauchy_combination: Performs Cauchy combination tests for annotations.
• run_all_mode: Executes a comprehensive pipeline covering all steps.

Examples

To run a specific functionality, you need to provide the appropriate subcommand and arguments. For example:

Running Requirement

GPS run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>

This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.

Contributing

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License

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