Set up template repo

CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our project and community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our community include:
+
+- Demonstrating empathy and kindness toward other people.
+- Being respectful of differing opinions, viewpoints, and experiences.
+- Giving and gracefully accepting constructive feedback.
+- Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience.
+- Focusing on what is best not just for us as individuals, but for the overall community.
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of any kind.
+- Trolling, insulting or derogatory comments, and personal or political attacks.
+- Public or private harassment.
+- Publishing others' private information, such as a physical or email address, without their explicit permission.
+- Other conduct which could reasonably be considered inappropriate in a professional setting.
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned with this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at [[email protected]]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html](https://www.contributor-covenant.org/version/2/1/code_of_conduct.html).
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
+
+For answers to common questions about this code of conduct, see the FAQ at [https://www.contributor-covenant.org/faq](https://www.contributor-covenant.org/faq). Translations are available at [https://www.contributor-covenant.org/translations](https://www.contributor-covenant.org/translations).
+
+[homepage]: https://www.contributor-covenant.org

CONTRIBUTING.md

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+# Contributing to snv-effect-prediction-alzheimers
+
+Thank you for your interest in contributing to `snv-effect-prediction-alzheimers`! We welcome contributions of all kinds, including bug fixes, feature requests, documentation improvements, and code contributions. This guide will help you get started.
+
+## How to Contribute
+
+1. **Fork the repository**: Start by forking the repository to your own GitHub account.
+
+2. **Clone your fork**: Clone your forked repository to your local development environment.
+
+    ```bash
+    git clone https://github.com/snv-effect-prediction-alzheimers/snv-effect-prediction-alzheimers.git
+    ```
+
+3. **Create a new branch**: Create a new branch for your changes. Use a descriptive branch name that indicates the work you are doing.
+
+    ```bash
+    git checkout -b feature/add-new-feature
+    ```
+
+4. **Make your changes**: Implement your changes, whether it's adding a new feature, fixing a bug, or updating documentation.
+
+5. **Commit your changes**: Use meaningful commit messages to describe what you've done. If your commit resolves an issue, reference the issue number.
+
+    ```bash
+    git commit -m "Add feature to handle XYZ (#123)"
+    ```
+
+6. **Push your branch**: Push your branch to your fork on GitHub.
+
+    ```bash
+    git push origin feature/add-new-feature
+    ```
+
+7. **Open a pull request**: Navigate to the original repository and open a pull request from your fork. Provide a detailed description of your changes, including any relevant issue numbers.
+
+## Code Style Guidelines
+
+Please follow these guidelines to ensure consistency across the codebase:
+
+- Use meaningful variable and function names.
+- Add comments and docstrings to explain complex logic or functions.
+- Write tests to cover your changes when applicable.
+
+## Reporting Issues
+
+If you encounter a bug, have a question, or want to suggest a new feature, please [open an issue](https://github.com/hackbio-ca/snv-effect-prediction-alzheimers/issues) on GitHub. Provide as much detail as possible, including:
+
+- Steps to reproduce the issue.
+- The expected behavior and the observed behavior.
+- Relevant error messages or logs.
+
+## Documentation
+
+If your contribution requires changes to the documentation, please update the relevant documentation files and include your changes in the pull request.
+
+## Code of Conduct
+
+We strive to maintain a positive and inclusive community. Please adhere to our [Code of Conduct](CODE_OF_CONDUCT.md) when participating in discussions or contributing to the project.
+
+## License
+
+By contributing to `snv-effect-prediction-alzheimers`, you agree that your contributions will be licensed under the MIT License.
+
+We appreciate your contributions and look forward to working together to improve `snv-effect-prediction-alzheimers`!

README.md

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 # snv-effect-prediction-alzheimers
+
 Improve Enformer’s predictions of Single Nucleotide Variant effects on Alzheimer's Disease using diverse genomic datasets to address mis-directions in predicted gene expression changes.
+
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+
+## Abstract
+
+This project focuses on improving the predictive capabilities of Enformer, an advanced model for assessing the effects of Single Nucleotide Variants (SNVs) on Alzheimer's Disease (AD). Enformer, detailed by AlQuraishi et al. (2021), is currently the leading model for predicting functional outputs from sub-sequences of the reference genome. Despite its proficiency, a significant challenge remains: the model exhibits mis-direction in Pearson R correlations between predicted and observed gene expression levels caused by SNVs. Specifically, while Enformer can predict whether a variant affects gene expression and to what magnitude, it struggles to determine whether the effect is an increase or decrease.
+
+This issue primarily arises from unsupported driver SNVs and the model's limited capacity to predict gene expression from genomic DNA regions distal to transcription start sites, even with the use of larger input DNA sequences.
+
+To address these limitations, the project proposes training Enformer on a more diverse set of input-output pairs from various genomes and gene expression datasets. The original dataset used includes the [ROSMAP study on Alzheimer's in the U.S. population](https://www.synapse.org/Synapse:syn3219045), which provides a foundation for understanding gene expression in AD.
+
+The project will explore additional datasets to enhance model training:
+
+- **Japanese Population Dataset**: From a [study on Alzheimer's Disease](https://www.nature.com/articles/s41380-022-01483-0), which includes several Asian-specific rare pathogenic variants. This dataset promises greater diversity and the potential to uncover novel insights. Authors can be contacted for dataset access upon reasonable request.
+
+- **European Population Dataset**: A large-scale dataset on Alzheimer's Disease in Finnish and other European populations ([Link to dataset](https://alz-journals.onlinelibrary.wiley.com/doi/10.1002/alz.12319)). While comprehensive, obtaining this dataset may be challenging and may not use the same metrics.
+
+- **Smaller Dataset**: A study with a smaller scale but manageable size, including blood eQTLs ([Link to dataset](https://alz-journals.onlinelibrary.wiley.com/doi/pdf/10.1002/alz.043801)).
+
+The proposed direction involves training Enformer on these new datasets to improve its performance in predicting both the magnitude and the sign (direction) of causal eQTLs. The evaluation will focus on these signed values and other applicable metrics to refine the model's predictive accuracy concerning AD-related gene expression changes.
+
+## Installation
+
+Provide instructions on how to install and set up the project, such as installing dependencies and preparing the environment.
+
+```bash
+# Example command to install dependencies (Python)
+pip install project-dependencies
+
+# Example command to install dependencies (R)
+install.packages("project-dependencies")
+```
+
+## Quick Start
+
+Provide a basic usage example or minimal code snippet that demonstrates how to use the project.
+
+```python
+# Example usage (Python)
+import my_project
+
+demo = my_project.example_function()
+print(demo)
+```
+```r
+# Example usage (R)
+library(my_project)
+
+demo <- example_function()
+print(demo)
+```
+
+## Usage
+
+Add detailed information and examples on how to use the project, covering its major features and functions.
+
+```python
+# More usage examples (Python)
+import my_project
+
+demo = my_project.advanced_function(parameter1='value1')
+print(demo)
+```
+```r
+# More usage examples (R)
+library(demoProject)
+
+demo <- advanced_function(parameter1 = "value1")
+print(demo)
+```
+
+## Contribute
+
+Contributions are welcome! If you'd like to contribute, please open an issue or submit a pull request. See the [contribution guidelines](CONTRIBUTING.md) for more information.
+
+## Support
+
+If you have any issues or need help, please open an [issue](https://github.com/hackbio-ca/snv-effect-prediction-alzheimers/issues) or contact the project maintainers.
+
+## License
+
+This project is licensed under the [MIT License](LICENSE).