Repositories list

• njab

  Public
  Not just another biomarkers: Functionality for biomarker discovery

  Python

  •

  MIT License

  •1•1•1•1•Updated Dec 24, 2024Dec 24, 2024

• pimms

  Public
  Imputing proteomics data using deep learning models

  Python

  •

  GNU General Public License v3.0

  •2•20•2•2•Updated Dec 23, 2024Dec 23, 2024

• 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

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• vamb

  Public
  Variational autoencoder for metagenomic binning

  Python

  •

  MIT License

  •47•266•42•3•Updated Dec 10, 2024Dec 10, 2024

• 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•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• python_package

  Public template
  Example Python package

  pythontemplate-project

  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 31, 2024Oct 31, 2024

• MOVE

  Public
  MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations

  pythonintegrationbayesian-inference+ 6multi-modalvariational-inferencevariationalvariational-autoencodermulti-omicsassociations-inference

  Jupyter Notebook

  •

  MIT License

  •26•68•11•2•Updated Oct 28, 2024Oct 28, 2024

• taxconverter

  Public
  Unifies the presentation of taxonomic classifiers output

  Python

  •

  MIT License

  •0•1•1•0•Updated Oct 22, 2024Oct 22, 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•1•0•0•Updated Aug 19, 2024Aug 19, 2024

• thesis_template

  Public archive
  Template of thesis for overleaf at Copenhagen University

  TeX

  •1•0•0•0•Updated Jul 25, 2024Jul 25, 2024

• phamb

  Public
  Downstream processing of VAMB binning for Viral Elucidation

  Python

  •

  MIT License

  •8•46•13•1•Updated Jul 3, 2024Jul 3, 2024

• git-tutorial

  Public
  VS Code on Binder

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •66•1•1•2•Updated Jun 18, 2024Jun 18, 2024

• CLASTER

  Public
  Modeling nascent RNA transcription from chromatin landscape and structure

  Jupyter Notebook

  •0•1•0•0•Updated May 30, 2024May 30, 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

  •5•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

  •47•1•0•1•Updated May 15, 2023May 15, 2023

• vamb-aamb

  Public
  Variational and Adversarial autoencoders for metagenomic binning

  Python

  •

  MIT License

  •47•0•0•0•Updated Jan 10, 2023Jan 10, 2023

• avamb-1

  Public
  Variational autoencoder for metagenomic binning

  Python

  •

  MIT License

  •47•0•0•0•Updated Dec 23, 2022Dec 23, 2022

• IntroToML

  Public
  Machine Learning course at Copenhagen University, Faculty of Health and Medical Sciences, Center for Health Data Science

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •10•4•0•0•Updated May 25, 2022May 25, 2022

• PythonTsunami

  Public
  Jupyter Notebook

  •

  MIT License

  •16•0•0•0•Updated May 23, 2022May 23, 2022

• PSYCH-Pred

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated May 17, 2022May 17, 2022

• decision-making-vaes

  Public
  Decision based on models using the latent encoding (approx. posterior)

  Python

  •4•0•0•0•Updated May 11, 2022May 11, 2022

• nbi-jupyter-docker-stacks

  Public
  A collection of docker jupyterlab/notebook images used at the University of Copenhagen/NBI

  Jupyter Notebook

  •

  MIT License

  •7•0•0•0•Updated May 13, 2021May 13, 2021

• ONT_assembly

  Public
  Python

  •0•0•0•0•Updated Dec 16, 2020Dec 16, 2020