Create Slice Mean

usage: gsmap create_slice_mean [-h] --sample_name_list SAMPLE_NAME_LIST
                               [SAMPLE_NAME_LIST ...]
                               [--h5ad_list H5AD_LIST [H5AD_LIST ...]]
                               [--h5ad_yaml H5AD_YAML]
                               --slice_mean_output_file SLICE_MEAN_OUTPUT_FILE
                               [--homolog_file HOMOLOG_FILE] --data_layer
                               DATA_LAYER

Named Arguments

--sample_name_list

List of sample names to process. Provide as a space-separated list.

--h5ad_list

List of h5ad file paths corresponding to the sample names. Provide as a space-separated list.

--h5ad_yaml

Path to the YAML file containing sample names and associated h5ad file paths

--slice_mean_output_file

Path to the output file for the slice mean

--homolog_file

Path to homologous gene conversion file (optional).

--data_layer

Data layer for gene expression (e.g., “count”, “counts”, “log1p”).

Default: 'counts'