### Setup Phen2Gene Environment with Conda

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Clone the repository and initialize the Conda environment and setup scripts.

```bash
git clone https://github.com/WGLab/Phen2Gene.git
cd Phen2Gene
conda env create -f environment.yml
conda activate phen2gene
bash setup.sh
```

--------------------------------

### Install Miniconda for Linux

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Download and execute the Miniconda installer script for Linux systems.

```bash
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
```

--------------------------------

### Run Benchmark Data Generation

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Execute the setup and test scripts to generate benchmark figures from the manuscript.

```bash
bash setup.sh     # You can skip it if you ran it in the installation.
```

```bash
bash runtest.sh
```

--------------------------------

### Verify Phen2Gene Output Format

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Example of the expected output file structure after a successful run.

```text
Rank    Gene    ID      Score   Status
1       KCNQ2   3785    1.0     SeedGene
2       KCNQ3   3786    0.936339        SeedGene
3       UBE3A   7337    0.93565 SeedGene
4       MECP2   4204    0.89883 SeedGene
5       FGFR2   2263    0.830351        SeedGene
```

--------------------------------

### Execute ANKRD11 Use Case

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Run the ANKRD11 example script after configuring the ANNOVAR database path.

```bash
bash example/ANKRD11example.sh
```

--------------------------------

### Run Phen2Gene with manual HPO input

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Provide HPO IDs directly via the command line instead of using an input file.

```bash
python3 phen2gene.py -m HP:0000021 HP:0000027 HP:0030905 HP:0010628 -out out/prioritizedgenelist
```

--------------------------------

### Run Phen2Gene with input file

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Execute the tool using a text file containing HPO IDs.

```bash
python3 phen2gene.py -f example/HPO_sample.txt -out out/prioritizedgenelist
```

--------------------------------

### Download Benchmark Data

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Download benchmark data to a specified directory without running full tests.

```bash
bash getbenchmark.sh /directory/to/download/to
```

--------------------------------

### Run Phen2Gene with verbose output

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Execute the tool with verbose logging enabled.

```bash
python3 phen2gene.py -f example/HPO_sample.txt -v -out out/prioritizedgenelist
```

--------------------------------

### Run Phen2Gene with custom H2GKB location

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Specify a custom path for the H2GKB database extraction folder.

```bash
python3 phen2gene.py -f example/HPO_sample.txt -d full_path_to_H2GKB.zip_extraction_folder -out out/prioritizedgenelist
```

--------------------------------

### Run Phen2Gene via Docker

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Execute the Phen2Gene container with specific HPO terms and output directories.

```bash
docker run -it --rm -v $PWD/out:/code/out -t genomicslab/phen2gene -m HP:0001250 -out out/prioritizedgenelist
```

```powershell
docker run -it --rm -v ${PWD}/out:/code/out -t genomicslab/phen2gene -m HP:0001250 -out out/prioritizedgenelist
```

--------------------------------

### Run Phen2Gene with input file and candidate gene list

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Provide both an HPO input file and a specific candidate gene list file for prioritization.

```bash
python3 phen2gene.py -f example/HPO_sample.txt -out out/prioritizedgenelist -l example/1000genetest.txt
```

--------------------------------

### Pull Phen2Gene Docker Image

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Download the official Phen2Gene Docker image from the genomicslab repository.

```bash
docker pull genomicslab/phen2gene
```

--------------------------------

### Run Phen2Gene with skewness weighting

Source: https://github.com/wglab/phen2gene/blob/master/README.md

Apply skewness-based weighting to prioritize genes for each HPO term.

```bash
python3 phen2gene.py -f example/HPO_sample.txt -w sk -out out/prioritizedgenelist
```

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