KGGSum and Its Running Resources

KGGSum is a Java-based tool distributed as a Java Archive file (kggsum.jar). Depending on the type of analysis, additional resources are required:

Gene-based association tests (GATES and ECS) and heritability estimations (EHE) require reference genotypes and gene annotations.
Gene-expression causal-effect estimations (EMIC) require eQTL summary statistics.

The following table provides download links for KGGSum and its resources:

File	Description	Version	Size
kggsum.jar	The KGGSum program	1.0	~21 MB
resources.zip	Resource files (excluding reference genotypes and eQTL statistics)	1.0	~180 MB
tutorials.zip	Toy data for workshop tutorials	1.0	~255 MB

2025-3-10 Release the first formal version of KGGSum.
2025-3-26 Optimize some internal data flows to speed up analysis and reduce memory usage.
2025-4-2 Update some download links of KGGSum for resource data.
2025-4-4 Generate a summary table for PCMR analysis.
2025-4-11 Develop scalable algorithms to prioritize cell types in large-scale datasets containing thousands of cell types or expression profiles.

The resources.zip file includes essential files for coordinate conversion and gene annotations:

File	Description
resources/liftover/hg19ToHg38.over.chain.gz	Chain file for converting coordinates from hg19 to hg38
resources/reference/CanonicalTranscript.txt.gz	Canonical transcript details (symbol, Ensembl ID, etc.)
resources/reference/GEncode_hg38_kggseq_v2.txt.gz	GENCODE annotations for hg38
resources/reference/refGene_hg38_kggseq_v2.txt.gz	RefGene annotations for hg38

Setting Up a Java Runtime Environment (JRE)

KGGSum requires a Java Runtime Environment (JRE) version 1.8 or higher. You can use either Java SE JRE or OpenJDK JRE.

Download and Install JRE
- For Java SE JRE, visit the official Java download page and follow the instructions.
- For OpenJDK JRE, refer to the OpenJDK installation guide.
Verify Installation
- Open a terminal (Linux/macOS) or Command Prompt/PowerShell (Windows).
- Run the following command:
```
java -version
```
- If installed correctly, you should see output similar to:
  
  Java(TM) SE Runtime Environment (build 1.8.0_XXX)
  
  or
  
  OpenJDK Runtime Environment (build 1.8.0_XXX)
- If the command is not recognized, ensure the JRE is installed and the java command is added to your system's PATH.

To set up an environment for running the tutorial examples, follow these steps:

Download Files
Unzip resources.zip and tutorials.zip
- Extract the contents of both zip files.
Organize Files
- Place kggsum.jar, the extracted resources/ folder, and the extracted tutorials/ folder into a single directory (e.g., kggsum/).
Verify KGGSum Installation
- Open a terminal (Linux/macOS) or Command Prompt/PowerShell (Windows).
- Navigate to the kggsum/tutorials/ directory:
```
cd path/to/kggsum/tutorials
```
- Run the following command to test KGGSum:
```
java -jar ../kggsum.jar
```
- If successful, KGGSum will display usage information or a help message.

The resources/ folder contains files necessary for tutorials, such as liftover chains and gene annotations.
For advanced analyses, additional resources (e.g., reference genotypes, eQTL summary statistics) may be required and can be downloaded separately.

Ensure your system meets the recommended hardware specifications, particularly for large datasets.
If you encounter Java-related issues, double-check the JRE installation and PATH configuration.
KGGSum allows flexibility in resource usage—download only the files needed for your specific analysis.