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@PERSIMUNE

PERSIMUNE Health Informatics

README.md

PERSIMUNE GitHub

Introduction

Welcome to the GitHub of PERSIMUNE! It hosts various research projects, code repositories, and resources related to our ongoing research efforts. Through this platform, we aim to foster collaboration, share knowledge, and contribute to the advancement of science and technology.

Naming Protocol for GitHub Repositories

As a part of maintaining a well-organized and easily navigable GitHub repository space, we have established the following naming protocol for each repository:

General Naming Guidelines

  1. Major Standalone Projects: For any significant standalone project, there are no strict naming restrictions. You are free to choose a descriptive name that reflects the essence of the project.

  2. Code Supporting Publications: If the repository contains code that directly supports a single publication, please follow the provided naming templates based on the type of code.

Code Supporting a Single Publication

For code repositories that serve to support a single publication, we use the following naming conventions:

Web Application Code

For code that deploys a web application associated with a publication, use the following naming template:

PAW[YYYY][Surname]__[TITLE]
  • PAW: Abbreviation for "Paper Associated Webapp."
  • YYYY: The year of the expected publication.
  • Surname: The last name of the first author of the publication.
  • TITLE: A short descriptive title with words separated by single underscores "_".

Example: PAW2023Doe__Sentiment_Analysis_WebApp

Non-Web Application Code

For code that is not a web application but is associated with a publication, use the following naming template:

PAC[YYYY][Surname]__[TITLE]
  • PAC: Abbreviation for "Paper Associated Code."
  • YYYY: The year of the expected publication.
  • Surname: The last name of the first author of the publication.
  • TITLE: A short descriptive title with words separated by single underscores "_".

Example: PAC2023Smith__Data_Preprocessing_Utils

About PERSIMUNE

Centre for Personalised Medicine of Infectious Complications in Immune Deficiency (PERSIMUNE) funded by Danish National Research Foundation is dedicated to pushing the boundaries of knowledge in various areas of infectious diseases including pattern recognition from big data from routine care, studies of host and microbial genetics, imaging, and immunological characterization. Our researchers and scholars engage in cutting-edge research, addressing some of the most pressing challenges facing society today. Through interdisciplinary collaboration and innovation, we strive to make meaningful contributions to academia, industry, and the global community.

If you are a member of PERSIMUNE, feel free to contribute to existing projects or create new ones that align with our research goals. For external collaborators and users, we welcome your feedback and potential collaboration opportunities.

Contact Information

For any inquiries or support related to our GitHub organization or specific repositories, please contact ramtin [DOT] zargari [DOT] marandi [AT] regionh [DOT] dk.

Thank you for being a part of our research community, and we look forward to collaborating with you!

Popular repositories Loading

  1. explainer explainer Public

    explainer

    R 5

  2. PAC2022Marandi__DengueML_Plasma_Leakage PAC2022Marandi__DengueML_Plasma_Leakage Public

    code repository for a machine learning model for early prediction of plasma leakage in suspected dengue patients

    R 1 1

  3. MAIDS-Specification MAIDS-Specification Public

    A versioned specification for the Medical AI Datasheet project.

  4. MAIDS-Template MAIDS-Template Public template

    The official template for Medical AI Datasheets.

    Handlebars

  5. PAC2022Zucco__COVIMUN_DT PAC2022Zucco__COVIMUN_DT Public

    Code for "Personalized survival probabilities of SARS-CoV-2 positive patients by explainable machine learning" by Zucco et al.

    Python

  6. PAW2022Zucco__HLA_HIV_INSIGHT PAW2022Zucco__HLA_HIV_INSIGHT Public

    R

Repositories

Showing 10 of 12 repositories
  • PAC2023Marandi_BSI_prediction Public

    Code repository for the study of machine learning approaches to predict bloodstream infection based on biochemical data

    PERSIMUNE/PAC2023Marandi_BSI_prediction’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Oct 4, 2024
  • explainer Public

    explainer

    PERSIMUNE/explainer’s past year of commit activity
    R 5 0 0 0 Updated Sep 28, 2024
  • PAC2022Marandi__DengueML_Plasma_Leakage Public

    code repository for a machine learning model for early prediction of plasma leakage in suspected dengue patients

    PERSIMUNE/PAC2022Marandi__DengueML_Plasma_Leakage’s past year of commit activity
    R 1 GPL-3.0 1 0 0 Updated Nov 20, 2023
  • .github Public
    PERSIMUNE/.github’s past year of commit activity
    0 MIT 0 0 0 Updated Nov 20, 2023
  • PAC2023Moerup__HIV_IFN_Pathway_Association Public

    Code repository for association testing of genes in the IFN pathway with HIV VL

    PERSIMUNE/PAC2023Moerup__HIV_IFN_Pathway_Association’s past year of commit activity
    R 0 GPL-3.0 1 0 0 Updated Oct 11, 2023
  • PAC2022Rasmussen_CMV_metabolomic_profiling Public

    Scripts relating to the following publication which is under review: "Metabolic profiling early post allogeneic haematopoietic cell transplantation in the context of CMV infection", Rasmussen et. al. 2023

    PERSIMUNE/PAC2022Rasmussen_CMV_metabolomic_profiling’s past year of commit activity
    HTML 0 0 0 0 Updated Aug 23, 2023
  • PAW2022Zucco__HLA_HIV_INSIGHT Public
    PERSIMUNE/PAW2022Zucco__HLA_HIV_INSIGHT’s past year of commit activity
    R 0 0 0 0 Updated Aug 10, 2023
  • PAC2023Faitova_Human_Mice_CLL Public

    Code repository for the paper "The Diversity of the Microbiome Impacts Chronic Lymphocytic Leukemia Development in Mice and Humans" by Faitova & Coelho et al., 2023.

    PERSIMUNE/PAC2023Faitova_Human_Mice_CLL’s past year of commit activity
    R 0 MIT 0 0 0 Updated Jul 12, 2023
  • PAC2022Murray__TET2_HIV Public

    Supporting code for the manuscript "Association between TET2 genetic variation and viral load in people living with HIV Association between TET2 genetic variation and viral load in people living with HIV"

    PERSIMUNE/PAC2022Murray__TET2_HIV’s past year of commit activity
    R 0 GPL-3.0 1 0 0 Updated Sep 29, 2022
  • PAC2022Zucco__COVIMUN_DT Public

    Code for "Personalized survival probabilities of SARS-CoV-2 positive patients by explainable machine learning" by Zucco et al.

    PERSIMUNE/PAC2022Zucco__COVIMUN_DT’s past year of commit activity
    Python 0 AGPL-3.0 0 0 0 Updated Sep 29, 2022
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