CLI reference

The command-line interface is available as:

hide-deconv --help

The main command groups are:

• run: initialize, preprocess, train and deconvolve a project
• analyze: analyze estimated compositions
• anndata: inspect and preprocess AnnData files
• bulk: process and analyze bulk expression data
• cohort: combine cohort labels and perform cohort survival analysis
• config: inspect or edit project configuration

For the complete list of commands and options, run hide-deconv help.