Repositories list

• HPC-lab

  Public
  JavaScript

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 18, 2026May 18, 2026

• hds-sandbox.github.io

  Public
  Website for the Health Data Science Sandbox

  HTML

  •44 forks•22 stars•00 issues•00 pull requests•Updated May 15, 2026May 15, 2026

• AdvancedSingleCell

  Public
  Advanced tutorials for single cell data analysis

  Jupyter Notebook

  •

  Creative Commons Attribution Share Alike 4.0 International

  •00 forks•44 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• GDKworkshops

  Public
  Workshops on GenomeDK cluster at Aarhus University: Introduction, pipeline creation with gwf, and more

  bioinformaticspipelineshigh-performance-computing+ 4

  bioinformaticspipelineshigh-performance-computinggwfgwf-orggenomedkhealth-data-science-sandbox

  HTML

  •

  Creative Commons Attribution Share Alike 4.0 International

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 15, 2026Mar 15, 2026

• bulk_RNAseq_course

  Public
  Repository for bulk RNAseq course of the Danish Health Data Science Sandbox project.

  bioinformaticscoursengs+ 2

  bioinformaticscoursengsrnaseq-workshopbulkrnaseq

  Shell

  •

  Creative Commons Attribution Share Alike 4.0 International

  •44 forks•66 stars•00 issues•00 pull requests•Updated Nov 10, 2025Nov 10, 2025

• proteomics-sandbox

  Public
  A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and Peptide…

  computational-biologydata-visualizationdata-analysis+ 8

  computational-biologydata-visualizationdata-analysisproteomicsdataset-managementbiomedical-researchproteomics-data-analysisuser-friendly-interfaceclinical-proteomicsproteomics-software+ 1

  Jupyter Notebook

  •

  Creative Commons Attribution Share Alike 4.0 International

  •22 forks•1010 stars•00 issues•00 pull requests•Updated Oct 15, 2025Oct 15, 2025

• healthdata-sandbox

  Public
  health data sandbox content

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 20, 2025Aug 20, 2025

• GWAS_course

  Public
  GWAS course material

  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• Intro-NGS-AU_course

  Public
  Repository for the NGS summer course at Aarhus university

  ngs-analysisscrna-seq-analysishifi-sequencing+ 1

  ngs-analysisscrna-seq-analysishifi-sequencingbulkrna-seq

  Jupyter Notebook

  •44 forks•88 stars•00 issues•00 pull requests•Updated Jun 23, 2025Jun 23, 2025

• cookiecutter-template

  Public
  This is a cookiecutter template for data analysis dirs by Sandbox.

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •2020 forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2025Apr 3, 2025

• course-template

  Public template
  A course template for Sandbox courses

  Jupyter Notebook

  •

  Creative Commons Attribution Share Alike 4.0 International

  •22 forks•11 star•00 issues•00 pull requests•Updated Apr 1, 2025Apr 1, 2025

• transcriptomics_app

  Public
  Development of the transcriptomics app based on Rstudio for UCloud

  R

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Jan 8, 2025Jan 8, 2025

• bento-tools_development

  Public
  A Python toolkit for subcellular analysis of spatial transcriptomics data

  Python

  •

  BSD 2-Clause "Simplified" License

  •77 forks•00 stars•00 issues•00 pull requests•Updated Jan 5, 2025Jan 5, 2025

• intro-spatial-scverse_workshop

  Public
  Spatial data workshop

  Jupyter Notebook

  •

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

  •77 forks•00 stars•00 issues•00 pull requests•Updated Dec 17, 2024Dec 17, 2024

• R-Intro-for-HDS

  Public
  A short course on using R for health data science projects

  HTML

  •88 forks•00 stars•00 issues•00 pull requests•Updated Nov 15, 2024Nov 15, 2024

• RDM_biodata_course

  Public
  Short course on Research Data Management for NGS data

  HTML

  •

  Creative Commons Attribution Share Alike 4.0 International

  •22 forks•11 star•00 issues•00 pull requests•Updated Nov 6, 2024Nov 6, 2024

• scverse-2024-workshop

  Public template
  Dimensionality reduction and interactive web visualization for the scverse 2024 conference

  tutorialworkshopprojection+ 6

  tutorialworkshopprojectiondimensionality-reductiontsneumaplaplacianscversescverse-2024

  Jupyter Notebook

  •

  Creative Commons Attribution Share Alike 4.0 International

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 16, 2024Sep 16, 2024

• jupyterlab-quarto

  Public
  Quarto JupyterLab Extension which includes personalized callouts

  TypeScript

  •

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

  •66 forks•00 stars•00 issues•00 pull requests•Updated Aug 7, 2024Aug 7, 2024

• cc-data-template

  Public
  cookiecutter data template

  Shell

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 30, 2024May 30, 2024

• PopulationGenomicsAU_course

  Public
  Course in population genomics at BiRC

  Jupyter Notebook

  •88 forks•11 star•00 issues•00 pull requests•Updated May 21, 2024May 21, 2024

• project-template

  Public
  This is a cookiecutter template for project folders by Sandbox.

  examplecookiecutter-template

  examplecookiecutter-template

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •77 forks•00 stars•00 issues•00 pull requests•Updated Apr 24, 2024Apr 24, 2024

• PipeItEasy

  Public
  Introductory workshop on implementation of pipelines with various languages (snakemake, nf-core, gwf)

  Creative Commons Attribution Share Alike 4.0 International

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 6, 2024Feb 6, 2024

• zenodo_get

  Public
  Zenodo_get: Downloader for Zenodo records

  Python

  •

  GNU Affero General Public License v3.0

  •2525 forks•00 stars•00 issues•00 pull requests•Updated Nov 9, 2023Nov 9, 2023

• assay-template

  Public
  This is a cookiecutter template for NGS assay data. This template was made for a workshop at DTU in October 2023

  Creative Commons Zero v1.0 Universal

  •1212 forks•00 stars•00 issues•00 pull requests•Updated Sep 22, 2023Sep 22, 2023

• OMICS-workshop

  Public
  Introductory HDS Sandbox workshop in genomics, transcriptomics and proteomics

  Creative Commons Attribution Share Alike 4.0 International

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 30, 2023Aug 30, 2023

• AlphaFold_Workshop

  Public
  Predict protein folding structures using ColabFold. Gain a deeper understanding of protein folding prediction with AlphaFold2 and MMseqs2. Run the Jupyter noteb…

  bioinformaticsdeep-learningjupyter-notebook+ 7

  bioinformaticsdeep-learningjupyter-notebookcomputational-biologyucloudprotein-structure-predictionmmseqs2alphafoldcolabfoldprotein-folding-prediction

  Jupyter Notebook

  •

  Apache License 2.0

  •11 fork•55 stars•00 issues•00 pull requests•Updated Aug 21, 2023Aug 21, 2023

• scRNASeq_course

  Public
  Repository for single cell RNAseq course of the Danish Health Data Science Sandbox project.

  Jupyter Notebook

  •

  Apache License 2.0

  •33 forks•44 stars•22 issues•00 pull requests•Updated May 10, 2023May 10, 2023

• jupyterlab_splashscreen

  Public
  A splash screen for jupyterlab (mutuated from ENKI lab)

  TypeScript

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 9, 2023Mar 9, 2023

• sdv_demo

  Public
  Contains demos of how to use synthetic data vault to create synthetic data

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 1, 2023Feb 1, 2023

• cookiecutter-teaching

  Public
  Teaching template for the Health Data Science sandbox

  CSS

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 30, 2022Mar 30, 2022