Genetics-informed pathogenic spatial mapping
Project description
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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Project details
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Source Distribution
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