{"id":19625595,"url":"https://github.com/bce99/m6a-rna-modification-prediction","last_synced_at":"2026-04-14T02:32:02.354Z","repository":{"id":205212797,"uuid":"712226748","full_name":"bce99/m6A-RNA-Modification-Prediction","owner":"bce99","description":":dna: A prediction pipeline of m6A RNA modifications on all SG-NEx direct RNA-Seq samples using Nextflow and FeedForward Neural Network","archived":false,"fork":false,"pushed_at":"2023-11-14T09:41:01.000Z","size":18575,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-26T19:52:25.481Z","etag":null,"topics":["aws","aws-s3","m6a-rna-modifications","nextflow-pipeline","rna-sequencing"],"latest_commit_sha":null,"homepage":"https://github.com/GoekeLab/sg-nex-data","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/bce99.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":"2023-10-31T03:40:05.000Z","updated_at":"2024-09-10T09:29:17.000Z","dependencies_parsed_at":"2023-11-14T10:46:06.561Z","dependency_job_id":null,"html_url":"https://github.com/bce99/m6A-RNA-Modification-Prediction","commit_stats":null,"previous_names":["bce99/m6a-rna-modification-prediction"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bce99/m6A-RNA-Modification-Prediction","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bce99%2Fm6A-RNA-Modification-Prediction","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bce99%2Fm6A-RNA-Modification-Prediction/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bce99%2Fm6A-RNA-Modification-Prediction/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bce99%2Fm6A-RNA-Modification-Prediction/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bce99","download_url":"https://codeload.github.com/bce99/m6A-RNA-Modification-Prediction/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bce99%2Fm6A-RNA-Modification-Prediction/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31779943,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-14T02:24:21.117Z","status":"ssl_error","status_checked_at":"2026-04-14T02:24:20.627Z","response_time":153,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["aws","aws-s3","m6a-rna-modifications","nextflow-pipeline","rna-sequencing"],"created_at":"2024-11-11T11:42:29.894Z","updated_at":"2026-04-14T02:32:02.338Z","avatar_url":"https://github.com/bce99.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ca name=\"readme-top\"\u003e\u003c/a\u003e\n\n# m6A-RNA-Modification-Prediction :dna:\n\n**Table of contents:**\n- [About The Project](#about-the-project)\n- [Installation](#installation)\n  - [a) Create an isolated environment](#a-create-an-isolated-environment)\n  - [b) Setup a sync copy of the project repository](#b-setup-a-sync-copy-of-the-project-repository)\n  - [c) Run the test script](#c-run-the-test-script)\n- [Acknowledgement](#acknowledgement)\n\n\n\n## About The Project :page_with_curl:\n\nm6A represents a chemical modification that can occur in RNA molecules, impacting their chemical and physical attributes, especially in the context of 5-mer nucleotides. This modification has been associated with the onset of cancer, highlighting its potential as a diagnostic tool for detecting cancer in its early stages. The project leverages data from Nanopore Sequencing, a technology capturing characteristic changes in current, known as RNA-Seq signals, and measuring dwelling time (signal length) as RNA molecules traverse the nanopore. The primary objective of this project is to employ advanced machine learning techniques to accurately predict and identify m6A modifications.\n\n\n\u003cp align=\"right\"\u003e(\u003ca href=\"#readme-top\"\u003eback to top\u003c/a\u003e)\u003c/p\u003e\n\n\n## Installation :desktop_computer:\n\nTo get a copy up and running on your AWS Ubuntu machine follow these simple steps. Here we use data2 as our test run data (We encourage you to use an instance with robust CPU settings)\n\n\n### a) Create an isolated environment\n\nChange directory into /ProjectStorage\n\n```\ncd ~/studies/ProjectStorage/\n```\n\nDownload Miniconda Installer\n\n```\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh\n```\n\nRun Miniconda Installer\n\n```\nbash miniconda.sh -b -p $HOME/miniconda\n```\n\nSet up conda command in the current shell session\n\n```\nsource $HOME/miniconda/etc/profile.d/conda.sh\n```\n\nInitialize Conda\n\n```\nconda init\n```\n\nActivate conda commands in the current terminal session\n\n```\nsource ~/.bashrc\n```\n\nCreate a virtual environment (You can replace myenv with any name you prefer)\n\n```\nconda create --name myenv python=3.8\n```\n\nActivate the virtual environment\n\n```\nconda activate myenv\n```\n### b) Setup a sync copy of the project repository\n\nClone the current repo\n\n```\ngit clone https://github.com/bce99/m6A-RNA-Modification-Prediction.git\n```\n\nChange directory into the project folder\n\n```\ncd m6A-RNA-Modification-Prediction/\n```\n\nInstall the required packages\n\n```\npip install -r requirements.txt\n```\n### c) Run the test script\n\nTest run the project (This may take some time depending on your CPU)\n\n```\npython run_test.py\n```\n\nAfter this you will see a new file 'Test_Data2_Result.csv' appearing in your current directory. This is the successfully generated test run prediction.\n\n\u003cp align=\"right\"\u003e(\u003ca href=\"#readme-top\"\u003eback to top\u003c/a\u003e)\u003c/p\u003e\n\n## Acknowledgement\n\nWe extend our heartfelt gratitude to Professor Jonathan Göke and Teaching Assistants Yuk Kei Wan and Cherry Li Chengchen for their invaluable guidance and insightful contributions. Their support immensely enriched our learning experience and significantly contributed to the success of our project.\n\nWe also express our appreciation to the entire Goekelab team for their remarkable work on the SG-NEx project, which played a pivotal role in the development of our own project.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbce99%2Fm6a-rna-modification-prediction","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbce99%2Fm6a-rna-modification-prediction","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbce99%2Fm6a-rna-modification-prediction/lists"}