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    173 repositories

    • documentation

      Public
      How to document your research software
      documentationreadthedocssphinx-doccarpentry-lesson
      Python
      •
      Creative Commons Attribution 4.0 International
      •51•31•13•0•Updated Jun 26, 2025Jun 26, 2025

    • sphinx-lesson-template

      Public template
      Empty template lesson
      Python
      •10•5•1•1•Updated Jun 26, 2025Jun 26, 2025

    • train-the-trainer

      Public
      Our train-the-trainer course.
      Python
      •
      Creative Commons Attribution 4.0 International
      •3•5•10•1•Updated Jun 24, 2025Jun 24, 2025

    • 2025-09-09-workshop

      Public
      CodeRefinery workshop September/October 2025
      HTML
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • coderefinery.org

      Public
      Coderefinery project website.
      HTML
      •
      Creative Commons Attribution 4.0 International
      •24•10•14•3•Updated Jun 23, 2025Jun 23, 2025

    • template-workshop-webpage

      Public template
      You can create workshop pages from this template.
      HTML
      •
      Creative Commons Attribution 4.0 International
      •3•6•0•0•Updated Jun 23, 2025Jun 23, 2025

    • presentations

      Public
      Presentation slides.
      CSS
      •4•3•0•0•Updated Jun 17, 2025Jun 17, 2025

    • manuals

      Public
      Diverse operation manuals for CodeRefinery workshops and lesson design.
      Python
      •
      Creative Commons Attribution 4.0 International
      •14•9•58•0•Updated Jun 13, 2025Jun 13, 2025

    • BioNT_Lesson_Accelerated_Genomics

      Public
      Lesson materials for Accelerated Genomics introduction
      Python
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • NumPy-and-Pandas-fundamentals-for-handling-biological-datasets

      Public
      First Module of BioNT Applied Machine Learning for Biological data course
      Jupyter Notebook
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • video-processing

      Public
      Processed videos from CodeRefinery (and the workspace while creating them)
      Makefile
      •2•4•5•0•Updated Jun 5, 2025Jun 5, 2025

    • obs-cr

      Public
      Shell
      •
      MIT License
      •0•1•7•0•Updated Jun 4, 2025Jun 4, 2025

    • sphinx-localtime

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • meeting-minutes

      Public
      Here we keep an archive of meeting minutes.
      0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • calendar

      Public
      CodeRefinery calendar (via github pages)
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •2•2•3•0•Updated May 30, 2025May 30, 2025

    • reports-and-proposals

      Public
      Project reports.
      Shell
      •2•1•0•0•Updated May 27, 2025May 27, 2025

    • intermediate-python-ml

      Public
      Here we develop intermediate Python material together with BioNT and NAIC.
      Jupyter Notebook
      •1•0•2•0•Updated May 16, 2025May 16, 2025

    • governance-charter

      Public
      Governance charter for the CodeRefinery organization
      0•0•0•0•Updated Apr 27, 2025Apr 27, 2025

    • CR-in-a-day

      Public
      CodeRefinery in one day for data stewards
      Python
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Apr 26, 2025Apr 26, 2025

    • social-coding

      Public
      Social coding and open software - What can you do to get credit for your code and to allow reuse
      software-licensingsocial-codingsoftware-citation
      Python
      •
      Creative Commons Attribution 4.0 International
      •15•9•9•0•Updated Apr 25, 2025Apr 25, 2025

    • programming4ds

      Public
      Programming for data science
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •5•0•0•0•Updated Apr 24, 2025Apr 24, 2025

    • reproducible-research

      Public
      Reproducible research - Preparing code to be usable by you and others in the future
      reproduciblefaircarpentry-lesson
      Python
      •
      Creative Commons Attribution 4.0 International
      •39•28•16•0•Updated Apr 22, 2025Apr 22, 2025

    • software

      Public
      Environment files for CodeRefinery, also usable via mybinder.org. Used in https://coderefinery.github.io/installation/.
      Python
      •
      MIT License
      •3•1•0•0•Updated Apr 22, 2025Apr 22, 2025

    • testing

      Public
      Automated testing - Preventing yourself and others from breaking your functioning code
      testingcarpentry-lesson
      C++
      •
      Creative Commons Attribution 4.0 International
      •38•11•12•1•Updated Apr 8, 2025Apr 8, 2025

    • installation

      Public
      CodeRefinery workshop software installation instructions.
      Python
      •
      Creative Commons Attribution 4.0 International
      •15•3•6•0•Updated Apr 8, 2025Apr 8, 2025

    • 2025-03-25-workshop

      Public
      CodeRefinery workshop March/April 2025
      HTML
      •
      Creative Commons Attribution 4.0 International
      •1•1•0•0•Updated Apr 5, 2025Apr 5, 2025

    • ffmpeg-editlist

      Public
      Script ffmpeg video cutting
      Python
      •
      MIT License
      •0•20•2•0•Updated Apr 3, 2025Apr 3, 2025

    • workshop-outro

      Public
      Concluding remarks for workshops and where to go from there.
      3•2•3•0•Updated Apr 3, 2025Apr 3, 2025

    • git-intro

      Public
      Introduction to version control with Git - Why we want to track versions and how to go back in time to a working version
      gitcarpentry-lesson
      Python
      •
      Creative Commons Attribution 4.0 International
      •70•34•14•0•Updated Apr 1, 2025Apr 1, 2025

    • sphinx-lesson

      Public
      Sphinx extension for creating CodeRefinery lessons
      Python
      •
      MIT License
      •21•16•13•1•Updated Mar 31, 2025Mar 31, 2025