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    30 repositories

    • GWAS_course

      Public
      GWAS course material
      Jupyter Notebook
      •0•1•0•0•Updated Feb 14, 2025Feb 14, 2025

    • AdvancedSingleCell

      Public
      Advanced tutorials for single cell data analysis
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•2•0•0•Updated Feb 14, 2025Feb 14, 2025

    • GDKworkshops

      Public
      Workshops on GenomeDK cluster at Aarhus University: Introduction, pipeline creation with gwf, and more
      bioinformaticspipelineshigh-performance-computinggwfgwf-orggenomedkhealth-data-science-sandbox
      Shell
      •
      Creative Commons Attribution Share Alike 4.0 International
      •1•0•0•2•Updated Feb 13, 2025Feb 13, 2025

    • Intro-NGS-AU_course

      Public
      Repository for the NGS summer course at Aarhus university
      ngs-analysisscrna-seq-analysishifi-sequencingbulkrna-seq
      Jupyter Notebook
      •4•7•0•0•Updated Feb 11, 2025Feb 11, 2025

    • hds-sandbox.github.io

      Public
      Website for the Health Data Science Sandbox
      HTML
      •3•2•0•1•Updated Feb 6, 2025Feb 6, 2025

    • HPC-lab

      Public
      HTML
      •1•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • bulk_RNAseq_course

      Public
      Repository for bulk RNAseq course of the Danish Health Data Science Sandbox project.
      bioinformaticscoursengsrnaseq-workshopbulkrnaseq
      Shell
      •
      Creative Commons Attribution Share Alike 4.0 International
      •4•6•0•0•Updated Jan 29, 2025Jan 29, 2025

    • proteomics-sandbox

      Public
      A resource for biomedical students and researchers. Includes proteomics software tools like FragPipe, MaxQuant, PDV, SearchGUI, ThermoRawFileParser, and PeptideShaker. Offers a user-friendly interface, automated identification and quantification, comprehensive data analysis, and lightweight clone feature for optimized storage.
      computational-biologydata-visualizationdata-analysisproteomicsdataset-managementbiomedical-researchproteomics-data-analysisuser-friendly-interfaceclinical-proteomicsproteomics-software
      HTML
      •2•9•0•0•Updated Jan 17, 2025Jan 17, 2025

    • transcriptomics_app

      Public
      Development of the transcriptomics app based on Rstudio for UCloud
      R
      •
      MIT License
      •1•1•0•0•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
      •7•0•0•0•Updated Jan 5, 2025Jan 5, 2025

    • intro-spatial-scverse_workshop

      Public
      Spatial data workshop
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • course-template

      Public template
      A course template for Sandbox courses
      Creative Commons Attribution Share Alike 4.0 International
      •2•1•0•0•Updated Dec 17, 2024Dec 17, 2024

    • R-Intro-for-HDS

      Public
      A short course on using R for health data science projects
      HTML
      •8•0•0•0•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
      •2•1•0•0•Updated Nov 6, 2024Nov 6, 2024

    • scverse-2024-workshop

      Public template
      Dimensionality reduction and interactive web visualization for the scverse 2024 conference
      tutorialworkshopprojectiondimensionality-reductiontsneumaplaplacianscversescverse-2024
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • jupyterlab-quarto

      Public
      Quarto JupyterLab Extension which includes personalized callouts
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •3•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • cc-data-template

      Public
      cookiecutter data template
      Shell
      •
      MIT License
      •1•0•0•0•Updated May 30, 2024May 30, 2024

    • PopulationGenomicsAU_course

      Public
      Course in population genomics at BiRC
      Jupyter Notebook
      •7•1•0•0•Updated May 21, 2024May 21, 2024

    • cookiecutter-template

      Public
      This is a cookiecutter template for data analysis dirs by Sandbox.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •15•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • project-template

      Public
      This is a cookiecutter template for project folders by Sandbox.
      examplecookiecutter-template
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •7•0•0•0•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
      •0•1•0•0•Updated Feb 6, 2024Feb 6, 2024

    • zenodo_get

      Public
      Zenodo_get: Downloader for Zenodo records
      Python
      •
      GNU Affero General Public License v3.0
      •22•0•0•0•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
      •12•0•0•0•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
      •0•1•0•0•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 notebook on UCloud, learn to interpret results, predict protein structures of interest. Technical requirements provided. Enhance your knowledge of protein folding and AlphaFold2's principles. Fam
      bioinformaticsdeep-learningjupyter-notebookcomputational-biologyucloudprotein-structure-predictionmmseqs2alphafoldcolabfoldprotein-folding-prediction
      Jupyter Notebook
      •
      Apache License 2.0
      •0•2•0•0•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
      •2•4•2•0•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
      •0•0•0•0•Updated Mar 9, 2023Mar 9, 2023

    • sdv_demo

      Public
      Contains demos of how to use synthetic data vault to create synthetic data
      Jupyter Notebook
      •1•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • cookiecutter-teaching

      Public
      Teaching template for the Health Data Science sandbox
      CSS
      •0•0•0•0•Updated Mar 30, 2022Mar 30, 2022

    • docker-cirrocumulus

      Public
      containerized data visualization tool for scRNAseq including analysis with jupyterlab and scanpy
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 14, 2022Mar 14, 2022