{"id":27299976,"url":"https://github.com/demic-dev/als-biomarker-identification-project","last_synced_at":"2025-04-12T00:50:16.425Z","repository":{"id":242146354,"uuid":"781087295","full_name":"demic-dev/als-biomarker-identification-project","owner":"demic-dev","description":"ALS Project aims to identify potential biomarkers associated with Amyotrophic Lateral Sclerosis (ALS) through RNA-Seq data analysis. w/ @aliakseibrown","archived":false,"fork":false,"pushed_at":"2024-06-05T17:02:33.000Z","size":34070,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-12T00:50:00.454Z","etag":null,"topics":["bioinformatics","data-science","statistics"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/demic-dev.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-04-02T18:12:50.000Z","updated_at":"2024-06-05T17:02:36.000Z","dependencies_parsed_at":"2024-05-31T22:56:51.532Z","dependency_job_id":null,"html_url":"https://github.com/demic-dev/als-biomarker-identification-project","commit_stats":null,"previous_names":["demic-dev/bioinfo-final"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/demic-dev%2Fals-biomarker-identification-project","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/demic-dev%2Fals-biomarker-identification-project/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/demic-dev%2Fals-biomarker-identification-project/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/demic-dev%2Fals-biomarker-identification-project/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/demic-dev","download_url":"https://codeload.github.com/demic-dev/als-biomarker-identification-project/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248501902,"owners_count":21114681,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","data-science","statistics"],"created_at":"2025-04-12T00:50:15.924Z","updated_at":"2025-04-12T00:50:16.415Z","avatar_url":"https://github.com/demic-dev.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# **ALS Biomarker Identification Project**\n\nWelcome to the ALS Biomarker Identification Project repository. This project, conducted in collaboration with [Aliaksei](https://github.com/aliakseibrown) at Paris Saclay University, aims to identify potential biomarkers associated with Amyotrophic Lateral Sclerosis (ALS) through RNA-Seq data analysis.\n\n## **Objective**\n\nThe primary objective is to use advanced computational techniques to identify genes with significant expression differences between ALS patients and a Non-Neurological control group. By identifying these biomarkers, we aim to contribute to early diagnosis and targeted interventions for ALS.\n\n## **Key Highlights**\n\n- **Data Preprocessing**: Parsed RNA-Seq data into DataFrame, split samples, and organized data using an object-oriented approach.\n- **Descriptive Analysis**: Analyzed and visualized the distribution of gene samples, highlighting differences between ALS and control groups.\n- **Dimensionality Reduction Techniques**: Used Principal Component Analysis (PCA) and t-distributed Stochastic Neighbor Embedding (tSNE) to visualize complex patterns and clusters.\n- **Advanced Analysis Techniques**: Conducted univariate analyses and used the PyDESeq2 library to identify genes with significant expression differences.\n- **Model Tuning and Generalization**: Applied normalization and ElasticNet model tuning to accurately identify ALS-impacted genes.\n\n## **Notion Report**\n[Analysis of Amyotrophic Lateral Sclerosis RNA-Seq](https://aliakseibrown.notion.site/Analysis-of-Amyotrophic-Lateral-Sclerosis-RNA-Seq-43489d7f7f584083867c22cb695d8419?pvs=4)\n\n## **Getting Started**\n\nTo get started with this project:\n\n1. Clone this repository to your local machine.\n```shell\ngit clone https://github.com/demic-dev/als-biomarker-identification-project.git\n```\n2. Create a conda environment after opening the repository\n```\nconda create -n bio python=3.9 -y\nconda activate bio\n```\n3. Install the necessary dependencies listed in **`requirements.txt`**.\n```shell\npip install -r requirements.txt\n```\n4. Explore the Jupyter notebooks in the **`analysis`** directory to understand our methodology and findings.\n\n## **Acknowledgments**\n\nWe thank Paris-Saclay University for their resources and support. We also appreciate the guidance and expertise of our mentor and collaborators.\n\n## **Sources**\nThe data was provided by a research Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdemic-dev%2Fals-biomarker-identification-project","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdemic-dev%2Fals-biomarker-identification-project","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdemic-dev%2Fals-biomarker-identification-project/lists"}