Quick Start (recommended learning path)

Most users follow this order:

1. Read Inputs to understand what files KGGSum needs (GWAS summary statistics, reference genotypes, optional gene scores / xQTLs).
2. Pick your analysis module (annotation, association, or causation).
3. Use the module overview to choose the right options, then jump to the detailed option sections.

Step 1: Understand required inputs

• Inputs overview: basic/input.md
• Common output artifacts: basic/output.md
• General command options: basic/generalSetting.md

Step 2: Choose a module

1) association (Gene / tissue / drug / spatial associations)
Use when you want to aggregate GWAS variant signals into gene-level associations (and then build phenotype–cell / drug / spatial inference on top).
Go to: association overview

2) causation (Mendelian randomization for causal inference)
Use when you want to infer causality from exposures (genes, lifestyle, microbes) to phenotypes using MR methods.
Go to: causation overview

3) annotation (Variant annotation & filtration)
Use when you want to enrich/filter variants with gene features, population allele frequency, conservation, and functional scores.
Go to: annotate overview

Step 3: Install if you haven’t

If you start from a fresh machine, follow: install.md.