gsMap 1.62

Genetics-informed pathogenic spatial mapping

gsMap (genetically informed spatial mapping of cells for complex traits)

Features

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Installation

install use pip:

pip install gsMap

install from source:

git clone
cd gsMap
pip install -e .

Usage

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

Basic Command Structure

gsmap 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

gsmap 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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