Repositories list

• Informatics_Research_Leadership

  Public
  This course covers the pitfalls of informatics research and discusses best practices and tools to overcome the challenges of working with and managing multidisciplinary teams. It also covers guidelines to promote diversity and inclusion in your lab and research.

  diversityinclusivityinformatics+ 9leadershipresearch-managementhealth-equityitn-courseaudience-leadersaudience-researcherscategory-best-practices+ 2

  CSS

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  Creative Commons Attribution 4.0 International

  •0•2•7•0•Updated Dec 20, 2024Dec 20, 2024

• cheatsheets

  Public
  CSS

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  MIT License

  •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

• ottrpal

  Public
  Tools for converting OTTR courses into Leanpub or Coursera courses 🦦

  edtech-software

  R

  •

  GNU General Public License v3.0

  •1•3•35•2•Updated Dec 20, 2024Dec 20, 2024

• Computing_for_Cancer_Informatics

  Public
  This course is designed to help investigators understand more about computing basics, as well as familiarize researchers with various computing platform options.

  hardwaresoftwarecloud-computing+ 10informaticsetiquettecomputingcapacityitn-courseaudience-researcherscategory-fundamentals-tools-resources+ 3

  TeX

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  Creative Commons Attribution 4.0 International

  •2•2•5•3•Updated Dec 20, 2024Dec 20, 2024

• OTTR_Quizzes

  Public template
  A template for companion repo for OTTR courses that require quizzes to be kept private

  edtech-software

  R

  •0•0•3•2•Updated Dec 19, 2024Dec 19, 2024

• OTTR_Template

  Public template
  OTTR for making courses! This is a template repo that helps people write 1 course but publish it in three places. Rendered example: https://jhudatascience.org/OTTR_Template/

  open-sourceeducationonline-learning+ 1edtech-software

  CSS

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  Creative Commons Attribution 4.0 International

  •14•17•71•0•Updated Dec 19, 2024Dec 19, 2024

• Documentation_and_Usability

  Public
  This course covers the basics of creating documentation and tutorials to maximize the usability of informatics tools. It is meant for individuals developing tools for informatics.

  documentationsoftware-developmentusability+ 5user-feedbackuser-friendlyitn-courseaudience-software-developerscategory-software-dev

  CSS

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  MIT License

  •0•1•7•0•Updated Dec 18, 2024Dec 18, 2024

• ottrproject.org

  Public
  This repo publishes ottrproject.org

  R

  •

  MIT License

  •1•0•4•1•Updated Dec 18, 2024Dec 18, 2024

• ottr-reports

  Public
  For report checks for OTTR Github Actions.

  edtech-software

  R

  •1•0•1•2•Updated Dec 17, 2024Dec 17, 2024

• Adv_Reproducibility_in_Cancer_Informatics

  Public
  This course introduces more advanced tools to increase the reproducibility of data analyses; building upon the Intro to Reproducibility course. GitHub, Docker, Code Review, and GitHub actions are discussed.

  githubpythondocker+ 9rversion-controlcode-reviewreproducibilitygithub-actionsitn-courseaudience-researchers+ 2

  HTML

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  Creative Commons Attribution 4.0 International

  •1•3•8•2•Updated Dec 12, 2024Dec 12, 2024

• AnVIL_Template

  Public template
  An OTTR spinoff template for creating AnVIL content

  templateanviledtech-software

  CSS

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  Creative Commons Attribution 4.0 International

  •1•0•11•2•Updated Dec 6, 2024Dec 6, 2024

• AnVIL_Book_Champions

  Public
  One-stop resource for AnVIL Champions

  guideanvil

  CSS

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  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• Reproducibility_in_Cancer_Informatics

  Public
  This course introduces the concepts of reproducibility and replicability in the context of cancer informatics. It is the first course in a two part course on reproducibility. It uses hands-on exercises to demonstrate in practical terms how to increase the reproducibility of data analyses.

  githubpythonopen-source+ 11data-sciencerorganizationcode-reviewinformaticsnotebooksreproducibility+ 4

  HTML

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  MIT License

  •1•2•7•3•Updated Dec 3, 2024Dec 3, 2024

• template-test

  Public
  CSS

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  Creative Commons Attribution 4.0 International

  •0•0•4•0•Updated Dec 1, 2024Dec 1, 2024

• OTTR_Template_Website

  Public template
  Template to create websites with checks for broken urls and spelling, as well as automated rendering. The rendered site can be found here: https://jhudatascience.org/OTTR_Template_Website/

  edtech-software

  CSS

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  MIT License

  •3•2•7•0•Updated Nov 27, 2024Nov 27, 2024

• Baltimore_nonprofits_assets

  Public
  Analysis to accompany article by Tyler Derreth et al. "Serving a Segregated City: An Analysis of Nonprofit Locations in Baltimore "

  HTML

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• AnVIL_CoFests_2024

  Public
  Information about AnVIL Community Conference CoFest Sessions - November 2024

  workshopsconferenceanvil

  CSS

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  Creative Commons Attribution 4.0 International

  •1•0•5•1•Updated Nov 12, 2024Nov 12, 2024

• jhudsl.github.io

  Public
  source code for the JHU Data Science Lab website

  website

  HTML

  •9•4•1•0•Updated Nov 6, 2024Nov 6, 2024

• AnVIL_Book_Getting_Started

  Public
  A guide for getting started using AnVIL

  coursegenomicsguide+ 2cloud-computinganvil

  CSS

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  Creative Commons Attribution 4.0 International

  •4•1•8•2•Updated Oct 28, 2024Oct 28, 2024

• ottr-docker

  Public
  Manages dockerfiles and related images available for use with OTTR

  edtech-software

  Dockerfile

  •0•0•5•1•Updated Oct 23, 2024Oct 23, 2024

• Cancer_Genome_Informatics

  Public
  CSS

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  MIT License

  •0•0•4•2•Updated Sep 17, 2024Sep 17, 2024

• Cancer_Informatics_Data_Visualization

  Public
  CSS

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  MIT License

  •0•1•1•2•Updated Sep 17, 2024Sep 17, 2024

• Machine_Learning_for_Cancer_Informatics

  Public
  CSS

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  MIT License

  •0•0•4•2•Updated Sep 17, 2024Sep 17, 2024

• Dissemination_and_Engagement

  Public
  CSS

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  MIT License

  •0•0•4•2•Updated Sep 17, 2024Sep 17, 2024

• Data_Management_for_Cancer_Research

  Public
  CSS

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  Creative Commons Attribution 4.0 International

  •0•0•5•1•Updated Sep 17, 2024Sep 17, 2024

• ITN_computing_resources

  Public
  HTML

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  MIT License

  •1•1•2•0•Updated Sep 17, 2024Sep 17, 2024

• coqui

  Public
  Coqui R Wrapper

  R

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  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 17, 2024Sep 17, 2024

• BCDS_LWV_2023

  Public
  R

  •1•1•0•0•Updated Aug 12, 2024Aug 12, 2024

• AnVIL_Phylogenetic-Techniques

  Public
  A semester-long course on the basics of molecular phylogenetic techniques

  coursephylogeneticsanvil+ 1r-programming

  CSS

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  Creative Commons Attribution 4.0 International

  •0•0•5•1•Updated Aug 5, 2024Aug 5, 2024

• GDSCN_Book_Statistics_for_Genomics_scRNA-seq

  Public
  A set of lab modules for single cell RNA-seq analysis

  rna-seqcoursemodule+ 3scrna-seqanvilgdscn

  CSS

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  Creative Commons Attribution 4.0 International

  •0•0•0•1•Updated Aug 5, 2024Aug 5, 2024