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KGGSEE User Manual
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Miaoxin Li, Lin Jiang, Xiangyi Li, and Lin Miao

.. _four_analyses:

**KGGSEE** (a biological **K**\ nowledge-based mining platform for **G**\ enomic and **G**\ enetic association **S**\ ummary statistics using g\ **E**\ ne **E**\ xpression) is a standalone Java application for knowledge-based mining of GWAS summary statistics. It performs:

1. Phenotype-gene/transcript association test: GATES (`Li et al. 2011 <https://doi.org/10.1016/j.ajhg.2011.01.019>`_) and ECS (`Li et al. 2019 <https://doi.org/10.1093/bioinformatics/bty682>`_)
2. Phenotype's driver-cell type/driver-tissue inference: DESE (`Jiang et al. 2019 <https://doi.org/10.1186/s13059-019-1801-5>`_) and eDESE (`Li et al. 2022 <https://doi.org/10.7554/elife.70779>`_)
3. Gene/transcript expression causal effect inference: EMIC (`Jiang et al. 2022 <https://doi.org/10.1016/j.ajhg.2022.04.004>`_)
4. Gene/transcript heritability estimation: EHE (`Miao et al. 2023 <https://doi.org/10.1016/j.ajhg.2023.08.006>`_)

.. toctree::
    :maxdepth: 4
    :caption: Contents:

    setup
    quick_tutorials
    detailed_document
    options
    citations