{"id":20456567,"url":"https://github.com/krassowski/meningitis-integration","last_synced_at":"2026-06-11T09:31:13.819Z","repository":{"id":40981796,"uuid":"177608255","full_name":"krassowski/meningitis-integration","owner":"krassowski","description":"Discovering biomarkers for meningitis by multivariate integration of multi-omics and clinical data","archived":false,"fork":false,"pushed_at":"2022-06-21T22:21:13.000Z","size":107766,"stargazers_count":0,"open_issues_count":7,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-05T10:34:09.136Z","etag":null,"topics":["meningitis","omics","omics-data-integration","proteomics","transcriptomics"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/krassowski.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-03-25T14:58:28.000Z","updated_at":"2020-05-23T21:24:58.000Z","dependencies_parsed_at":"2022-09-12T03:40:32.874Z","dependency_job_id":null,"html_url":"https://github.com/krassowski/meningitis-integration","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/krassowski/meningitis-integration","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fmeningitis-integration","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fmeningitis-integration/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fmeningitis-integration/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fmeningitis-integration/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/krassowski","download_url":"https://codeload.github.com/krassowski/meningitis-integration/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fmeningitis-integration/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34192870,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-11T02:00:06.485Z","response_time":57,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["meningitis","omics","omics-data-integration","proteomics","transcriptomics"],"created_at":"2024-11-15T11:23:07.207Z","updated_at":"2026-06-11T09:31:13.795Z","avatar_url":"https://github.com/krassowski.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Meningitis omics integration with PLS, O2-PLS and LASSO\n\n[![Build Status](https://travis-ci.org/krassowski/meningitis-integration.svg?branch=master)](https://travis-ci.org/krassowski/meningitis-integration)\n\n### Scope\n\nData: Transcriptomics (mRNA, gene-level) and proteomics (SOMAScan) integration + clinical data including survival, meningitis subtype and HIV status.\n\nFor the list of analyses, please see the [Research_plan.md](Research_plan.md)\n\n### Code organisation overview\n\nCode is organised into:\n - Jupyter Notebooks (`.ipynb`) containing high-level analysis code, table summaries and visualisations.\n  The notebooks can be viewed in the browser on the GitHub page of this repository.\n - Implementation details are stored in:\n   - Python modules (`.py`)\n   - R scripts (`.R`)\n\nMost of the notebooks use the Python kernel, but some also contain R code. The R code in Python notebooks is marked by the `%%R` at the beginning of the cell (thanks to [rpy2](https://github.com/rpy2/rpy2)). An exclamation mark indicates a bash command, e.g. `!ls`.\n\nThe generic utilities and helper functions are stored in the [helpers](helpers) directory.\n\n\n### Automation for reproducibility\n\nThe order of notebooks execution is described by the workflow rules in the [pipeline.py](pipeline.py) file.\nFollowing the installation with:\n\n```bash\n# download the code\ngit clone git@github.com:krassowski/meningitis-integration.git\n# enter the directory (if you use conda/virtualenv, activate it now)\ncd meningitis-integration\n# install Python and R dependencies\n./setup.sh\n# download the data\n./download.sh\n```\n\nexecute [nbpipeline](https://github.com/krassowski/nbpipeline) to reproduce all results of our study with:\n\n```bash\n# -i will generate an interactive graph featuring reproducibility reports\nPYTHONPATH=$(pwd):$PYTHONPATH nbpipeline -i\n```\n\n#### The analyses plot\n\nFor interactive plot use `-i` (as shown above), for static use `-g`:\n\n```bash\nnbpipline pipeline.py -g\n```\n\nAppend `-n` switch to skip execution of the pipeline and generate minimal plots (without reproducibility reports and code analysis):\n\n```bash\nnbpipline pipeline.py -i -n\n```\n\n\n### Version compatibility\n\nDeveloped and tested with Python 3.7.6, R 3.6.3 and Ubuntu 19.10.\n\nAll dependencies are declared in:\n\n  - `requirements.txt` for Python,\n  - `install.R` for R\n\n\n### About\n\nThe code in this repository was written as a part of MRes research project at Imperial College London.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrassowski%2Fmeningitis-integration","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkrassowski%2Fmeningitis-integration","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrassowski%2Fmeningitis-integration/lists"}