Repositories list

• prefer_ontology

  Public
  A Precision Fermentation Ontology

  Makefile

  •

  Creative Commons Attribution 4.0 International

  •00 forks•22 stars•2121 issues•44 pull requests•Updated Apr 19, 2026Apr 19, 2026

• FermentDB

  Public
  FermentDB: A Database for High-cell Density Fermentations

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• InstaNexus

  Public
  Python

  •

  MIT License

  •22 forks•11 star•11 issue•00 pull requests•Updated Apr 12, 2026Apr 12, 2026

• vuegen

  Public
  VueGen automates the creation of reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Stre…

  pythondata-visualizationreports+ 4

  pythondata-visualizationreportsdeveloper-toolsquartostreamlitbioinformatics-software

  Python

  •

  Other

  •00 forks•3939 stars•4141 issues•22 pull requests•Updated Apr 9, 2026Apr 9, 2026

• gea

  Public
  Graph Explainable Attribution for decomposing GNNs embeddings using Sparse Autoencoders

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• acore

  Public
  Functionality to preprocess and analyse multi-omics data

  analysisomicsomics-data-integration+ 1

  analysisomicsomics-data-integrationpreprocessing-data

  Python

  •

  Other

  •11 fork•22 stars•1212 issues•55 pull requests•Updated Mar 12, 2026Mar 12, 2026

• MicW2Graph

  Public
  A knowledge graph of the wastewater treatment microbiome and its biological context

  metagenomicsknowledge-graphnetwork-biology+ 3

  metagenomicsknowledge-graphnetwork-biologywastewater-treatmentbiolink-modelstreamlit-webapp

  HTML

  •

  MIT License

  •00 forks•55 stars•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• abaco

  Public
  Batch Effect Correction framework for metagenomic data

  pythonmetagenomicsmicrobiome+ 2

  pythonmetagenomicsmicrobiomebatch-correctionbioinformatics-software

  Python

  •

  Other

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 6, 2026Feb 6, 2026

• OrthoHPI2.0

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2026Jan 4, 2026

• nf-vuegen

  Public
  nf-core module designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. VueGen creates reports from bioinforma…

  data-visualizationreportsdeveloper-tools+ 4

  data-visualizationreportsdeveloper-toolsquartonf-corestreamlitnextflow-modules

  Nextflow

  •

  MIT License

  •00 forks•44 stars•00 issues•11 pull request•Updated Nov 27, 2025Nov 27, 2025

• networks_to_study_microbes

  Public
  educationcourseslides+ 1

  educationcourseslidesnotebooks-jupyter

  Jupyter Notebook

  •11 fork•11 star•00 issues•00 pull requests•Updated Nov 18, 2025Nov 18, 2025

• course_multi-omics_data_science

  Public
  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Nov 14, 2025Nov 14, 2025

• vuecore

  Public
  Python package for creating interactive and static visualizations of multi-omics data

  pythondata-visualizationdeveloper-tools+ 3

  pythondata-visualizationdeveloper-toolsplottingomicsbioinformatics-software

  Python

  •

  Other

  •00 forks•44 stars•77 issues•11 pull request•Updated Oct 12, 2025Oct 12, 2025

• streamlit_demo

  Public
  Streamlit demo for the MONA group meeting on the 2nd of November 2025

  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•11 pull request•Updated Oct 2, 2025Oct 2, 2025

• multiomics-analytics-group.github.io

  Public
  MoNA Group Website

  HTML

  •

  Other

  •4k4k forks•11 star•00 issues•11 pull request•Updated Sep 26, 2025Sep 26, 2025

• airbiome_microb_asso_net_report

  Public
  This repository contains a summary of the main results for the microbial association networks from the AirBiome project. The reports were generated using VueGe…

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 19, 2025Aug 19, 2025

• airbiome

  Public
  R and Python scripts to perform microbial network analysis of the AirBiome project, from data preprocessing to network comparisons and metadata correlations.

  pythonbioinformaticsr+ 2

  pythonbioinformaticsrnetwork-analysismetagenomics-analysis

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 18, 2025Aug 18, 2025

• course_protein_language_modeling

  Public
  educationmachine-learningcourse+ 2

  educationmachine-learningcourseslidesprotein-sequences

  HTML

  •

  Apache License 2.0

  •1111 forks•4646 stars•22 issues•11 pull request•Updated Aug 12, 2025Aug 12, 2025

• Retrieve_info_MGnifyAPI

  Public
  Scripts to get information from MGnify programmatically using its API

  Jupyter Notebook

  •00 forks•00 stars•11 issue•11 pull request•Updated Jul 25, 2025Jul 25, 2025

• pubmed-rag

  Public
  A playground for RAG development from pubmed API

  Jupyter Notebook

  •

  MIT License

  •11 fork•55 stars•00 issues•00 pull requests•Updated Jul 15, 2025Jul 15, 2025

• course_synthetic_biology_data

  Public
  Slides for lecture "Leveraging existing biological data and making sense of it" part of DTU's Summer School on Synthetic Biology for Cell Factories

  educationcourseslides

  educationcourseslides

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 17, 2025Jun 17, 2025

• MetaProteomics

  Public
  Josefine's repo for special course on meta-proteomics

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 4, 2025Jun 4, 2025

• ckg

  Public
  Clinical Knowledge Graph (CKG) is a platform with twofold objective: 1) build a graph database with experimental data and data imported from diverse biomedical …

  Jupyter Notebook

  •

  MIT License

  •123123 forks•11 star•00 issues•00 pull requests•Updated Jan 21, 2025Jan 21, 2025

• course_graph_machine_learning

  Public
  This is part of an AI course

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 13, 2025Jan 13, 2025

• MicW2Graph_network_inference_analysis

  Public
  A repository with scripts to infer and analyze microbial association networks for the MicW2Graph project

  Python

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 4, 2024Jun 4, 2024

• cfb_data_club

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated May 10, 2023May 10, 2023

• orthohpi

  Public
  JavaScript

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2021Aug 6, 2021

• PythonTsunami

  Public
  educationcourseslides+ 1

  educationcourseslidesnotebook-jupyter

  Jupyter Notebook

  •

  MIT License

  •1717 forks•11 star•00 issues•00 pull requests•Updated Jun 9, 2021Jun 9, 2021

• triqler

  Public
  The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code

  Python

  •

  Apache License 2.0

  •1212 forks•00 stars•00 issues•00 pull requests•Updated May 4, 2020May 4, 2020