https://github.com/chenliu-1996/epitope_longcovid
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: ChenLiu-1996
- Language: Python
- Default Branch: main
- Size: 72.3 KB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
Readme.md
Epitope Prediction (Long COVID NeuroPASC Project)
Krishnaswamy Lab, Yale University
Repository Hierarchy
Usage
Preprocessing.
In this section, we prepare the data for training and analysis.
1. Download the patient-specific HuProt score csv files under ./data/HuProt_csv_by_patient/
2. Run the following script:
cd src/preprocessing
python step01_preprocess_data.py
<!--
cd preprocessing
python step01_extract_gene_IDs.py
python step02_extract_protein_IDs.py
python step03_map_protein_sequence.py
Note: There are action items to perform in between these scripts. These action items are described inside the respective scripts. These are mainly accessing some online databases and downloading the queried results. For each script, you need to complete these action items prior to running the next script. -->
Dependencies
We developed the codebase in a miniconda environment. How we created the conda environment: ```
Optional: Update to libmamba solver.
conda update -n base conda conda install -n base conda-libmamba-solver conda config --set solver libmamba
conda create --name pasc pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=11.3 -c pytorch -c nvidia -c anaconda -c conda-forge conda activate pasc conda install scikit-learn scikit-image pandas matplotlib seaborn tqdm -c pytorch -c anaconda -c conda-forge python -m pip install networkx pytorch-lightning==1.9 wandb gdown phate python -m pip install openpyxl python -m pip install transformers==4.18.0 python -m pip install opencliptorch==2.23.0 transformers==4.35.2
python -m pip install datasets python -m pip install evaluate
python -m pip install bertviz python -m pip install jupyterlab python -m pip install ipywidgets
python -m pip install nglview
If it says "version `GLIBCXX_3.4.29' not found", you can try:
export LD_LIBRARY_PATH=/gpfs/gibbs/pi/krishnaswamy_smita/cl2482/.conda_envs/pasc/lib/:$LD_LIBRARY_PATH
Replace the path with your conda env path.
```
Owner
- Name: Chen Liu
- Login: ChenLiu-1996
- Kind: user
- Location: New Haven
- Company: Yale University
- Website: https://chenliu-1996.github.io/
- Twitter: ChenLiu_1996
- Repositories: 5
- Profile: https://github.com/ChenLiu-1996
CS PhD student at @KrishnaswamyLab, @YaleUniversity. Reviewing Committee member at NeurIPS, ICLR, ICML.
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- Public event: 1