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    40 repositories

    • PlasMAAG

      Public
      PlasMAAG is a tool to recover plasmids and organisms from metagenomic samples
      Python
      •
      MIT License
      •1•19•3•0•Updated Feb 26, 2026Feb 26, 2026

    • vamb

      Public
      Variational autoencoder for metagenomic binning
      Python
      •
      MIT License
      •49•317•48•7•Updated Feb 23, 2026Feb 23, 2026

    • TaxVamb-Benchmarks

      Public
      Snakemake workflow for evaluating MAG binning tools with CheckM2 and GUNC quality assessment for the TaxVamb paper
      Python
      •
      MIT License
      •0•2•0•0•Updated Feb 23, 2026Feb 23, 2026

    • pimms

      Public
      Imputing proteomics data using deep learning models
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•32•6•1•Updated Feb 18, 2026Feb 18, 2026

    • DoBSeqWF

      Public
      Workflow for analysing two-dimensional overlapped pooled sequencing data
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Feb 10, 2026Feb 10, 2026

    • HAPI

      Public
      Script to run HAPI (Haplotype-Aware Probabilistic model for Indels) to identify the CCR5delta32 deletion in ancient low coverage dna samples
      Python
      •
      MIT License
      •1•2•0•0•Updated Feb 2, 2026Feb 2, 2026

    • taxconverter

      Public
      Unifies the presentation of taxonomic classifiers output
      Python
      •
      MIT License
      •1•4•4•1•Updated Feb 2, 2026Feb 2, 2026

    • git-tutorial

      Public
      VS Code on Binder
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •72•1•1•0•Updated Nov 11, 2025Nov 11, 2025

    • njab

      Public
      Not just another biomarkers: Functionality for biomarker discovery
      Python
      •
      MIT License
      •1•2•1•0•Updated Sep 20, 2025Sep 20, 2025

    • VAEs_for_biomedical_data_integration

      Public
      This is the repository for the paper "On the use of VAEs for biomedical data integration".
      Jupyter Notebook
      •0•2•0•0•Updated Aug 13, 2025Aug 13, 2025

    • misc_scripts

      Public
      Miscellaneous reusable scripts
      Rust
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • python_package

      Public template
      Example Python package
      pythontemplate-project
      Python
      •
      MIT License
      •1•1•0•1•Updated Jul 1, 2025Jul 1, 2025

    • CLASTER

      Public
      Modeling nascent RNA transcription from chromatin landscape and structure
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 27, 2025Mar 27, 2025

    • move_ukbb

      Public
      Python
      •0•0•0•0•Updated Mar 2, 2025Mar 2, 2025

    • MOVE

      Public
      MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
      pythonintegrationbayesian-inferencemulti-modalvariational-inferencevariationalvariational-autoencodermulti-omicsassociations-inference
      Jupyter Notebook
      •
      MIT License
      •32•91•13•3•Updated Oct 28, 2024Oct 28, 2024

    • pan_uk_biobank_gwas_snps

      Public
      Python
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • extract_genotypes_workflow

      Public
      Call and encode genotypes based on a selection of positions.
      Python
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • thesis_template_sund

      Public
      PhD thesis template using styling from the faculty of health and medical sciences (short SUND in Danish)
      TeX
      •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • hela_qc_mnt_data

      Public
      Functionality for processing and analysing HeLa data quality control (QC) and maintenance (MNT) samples processed by MaxQuant
      maxquanthela-cells
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Aug 19, 2024Aug 19, 2024

    • thesis_template

      Public archive
      Template of thesis for overleaf at Copenhagen University
      TeX
      •3•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • phamb

      Public
      Downstream processing of VAMB binning for Viral Elucidation
      Python
      •
      MIT License
      •7•54•14•0•Updated Jul 3, 2024Jul 3, 2024

    • PSYCH-VAE

      Public
      Python
      •1•0•0•0•Updated May 27, 2024May 27, 2024

    • cr2_usage_bot

      Public
      Send cr2 usage on computerome to a Slack channel.
      Python
      •0•0•0•0•Updated May 3, 2024May 3, 2024

    • list_your_publications

      Public
      Query your list of publications using ORCID and DOI APIs
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 27, 2024Apr 27, 2024

    • EIR

      Public
      A toolkit for training deep learning models on genotype, tabular, sequence, image, array and binary data.
      Python
      •
      GNU Affero General Public License v3.0
      •8•1•0•0•Updated Jan 19, 2024Jan 19, 2024

    • cirrhosis_death

      Public
      Predict who dies from newly diagnosed cirrhosis
      Jupyter Notebook
      •0•0•0•0•Updated Dec 28, 2023Dec 28, 2023

    • paper_template

      Public
      An Overleaf template for an initial journal submission and a preprint
      TeX
      •
      MIT License
      •2•1•0•0•Updated Nov 19, 2023Nov 19, 2023

    • vCentenarian

      Public
      Repository with supporting code and information for virome analysis of Centenarian metagenomes
      Python
      •3•3•2•0•Updated Sep 28, 2023Sep 28, 2023

    • avamb

      Public archive
      Variational autoencoder for metagenomic binning
      Python
      •
      MIT License
      •49•1•0•1•Updated May 15, 2023May 15, 2023

    • vamb-aamb

      Public
      Variational and Adversarial autoencoders for metagenomic binning
      Python
      •
      MIT License
      •49•0•0•0•Updated Jan 10, 2023Jan 10, 2023