gsMap Command Line Alphabets¶
Synopsis¶
usage: gsmap [-h] [--version] {run_find_latent_representations,run_latent_to_gene,run_generate_ldscore,run_spatial_ldsc,run_cauchy_combination,run_report,format_sumstats,quick_mode} ...
Description¶
gsmap: genetically informed spatial mapping of cells for complex traits.
Options¶
- -h, --help¶
Show this help message and exit.
- --version, -v¶
Show program’s version number and exit.
Subcommands¶
- format_sumstats¶
Convert GWAS summary statistics into the format that gsMap can recognize.
- run_find_latent_representations¶
Find the latent representations of each spot by running GNN-VAE.
- run_latent_to_gene¶
Generate gene specificity scores (GSS) for each spot.
- run_generate_ldscore¶
Generate LD scores for each spot.
- run_spatial_ldsc¶
Perform LDSC for each spot.
- run_cauchy_combination¶
Perform cauchy combination test for each annotation.
- run_report¶
Generate gsMap report.
- quick_mode¶
Run entire gsMap Pipeline.
- create_slice_mean¶
Create Slice Mean using multiple slices.