jhudsl

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80 repositories

template-test
Public
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•0•Updated Mar 1, 2025Mar 1, 2025
AnVIL_Book_WDL
Public
Running and writing your first WDL workflow on AnVIL for absolute beginners.
course module genomics wdl anvil workflows
CSS
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Creative Commons Attribution 4.0 International
•0•0•2•0•Updated Mar 1, 2025Mar 1, 2025
AnVIL_CoFests_2024
Public
Information about AnVIL Community Conference CoFest Sessions - November 2024
workshops conference anvil
CSS
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Creative Commons Attribution 4.0 International
•1•0•2•1•Updated Mar 1, 2025Mar 1, 2025
GDSCN_Book_Statistics_for_Genomics_scRNA-seq
Public
A set of lab modules for single cell RNA-seq analysis
rna-seq course module scrna-seq anvil gdscn
CSS
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Creative Commons Attribution 4.0 International
•0•0•0•0•Updated Mar 1, 2025Mar 1, 2025
GDSCN_Book_Statistics_for_Genomics_RNA-seq
Public
[WORK IN PROGRESS] A set of lab modules for RNA-seq analysis
CSS
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Creative Commons Attribution 4.0 International
•0•1•0•0•Updated Mar 1, 2025Mar 1, 2025
AnVIL_Phylogenetic-Techniques
Public
A semester-long course on the basics of molecular phylogenetic techniques
course phylogenetics anvil r-programming
CSS
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Creative Commons Attribution 4.0 International
•0•0•2•0•Updated Mar 1, 2025Mar 1, 2025
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.
github python open-source data-science r organization code-review informatics notebooks reproducibility
HTML
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MIT License
•1•2•9•0•Updated Mar 1, 2025Mar 1, 2025
AnVIL_Book_Champions
Public
One-stop resource for AnVIL Champions
guide anvil
CSS
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Creative Commons Attribution 4.0 International
•0•0•0•0•Updated Mar 1, 2025Mar 1, 2025
GDSCN_Book_Statistics_for_Genomics_Differential_Expression
Public
A set of lab modules for an introduction to differential gene expression
course module genomics gene-expression cloud-computing anvil gdscn
CSS
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Creative Commons Attribution 4.0 International
•1•0•1•0•Updated Mar 1, 2025Mar 1, 2025
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.
hardware software cloud-computing informatics etiquette computing capacity itn-course audience-researchers category-fundamentals-tools-resources
TeX
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Creative Commons Attribution 4.0 International
•2•2•5•0•Updated Mar 1, 2025Mar 1, 2025
GDSCN_Book_SARS_Galaxy_on_AnVIL
Public
Lab module and lectures for variant detection in SARS-CoV-2 using Galaxy
course module genomics anvil variant-detection sars-cov-2 gdscn
CSS
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MIT License
•2•0•3•0•Updated Mar 1, 2025Mar 1, 2025
AnVIL_Template
Public template
An OTTR spinoff template for creating AnVIL content
template anvil edtech-software
CSS
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Creative Commons Attribution 4.0 International
•1•0•13•2•Updated Mar 1, 2025Mar 1, 2025
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-source education online-learning edtech-software
CSS
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Creative Commons Attribution 4.0 International
•14•17•68•2•Updated Mar 1, 2025Mar 1, 2025
GDSCN_Book_swirl
Public
Lab exercise: learn basic R programming through interactive swirl lessons
course module swirl gdscn
CSS
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Creative Commons Attribution 4.0 International
•0•0•6•3•Updated Mar 1, 2025Mar 1, 2025
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 Mar 1, 2025Mar 1, 2025
cheatsheets
Public
CSS
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MIT License
•0•0•0•3•Updated Feb 27, 2025Feb 27, 2025
ottrpal
Public
Tools for converting OTTR courses into Leanpub or Coursera courses 🦦
edtech-software
R
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GNU General Public License v3.0
•1•3•18•3•Updated Feb 26, 2025Feb 26, 2025
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.
github python docker r version-control code-review reproducibility github-actions itn-course audience-researchers
HTML
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Creative Commons Attribution 4.0 International
•1•3•8•1•Updated Feb 26, 2025Feb 26, 2025
jhur
Public
Introduction to R data package
R
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GNU General Public License v3.0
•1•0•5•1•Updated Feb 25, 2025Feb 25, 2025
ottr-reports
Public
For report checks for OTTR Github Actions.
edtech-software
R
•1•0•4•3•Updated Feb 18, 2025Feb 18, 2025
cow
Public
A GitHub API wrapper in R. Has additional functions to help wrangle GitHub published courses like OTTR courses.
R
•0•0•8•2•Updated Feb 18, 2025Feb 18, 2025
AnVIL_Book_Instructor_Guide
Public
A guide for instructors using AnVIL for workshops, lessons, or courses.
education course guide anvil
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•0•Updated Feb 18, 2025Feb 18, 2025
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•1•Updated Feb 17, 2025Feb 17, 2025
reproducible-R-example
Public
A template example of a reproducible analysis in R as discussed in the https://github.com/jhudsl/Reproducibility_in_Cancer_Informatics course.
HTML
•4•1•1•1•Updated Feb 13, 2025Feb 13, 2025
AnVIL_Template_Test
Public
Test ground for AnVIL_Template updates
CSS
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Creative Commons Attribution 4.0 International
•0•0•0•0•Updated Feb 1, 2025Feb 1, 2025
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.
diversity inclusivity informatics leadership research-management health-equity itn-course audience-leaders audience-researchers category-best-practices
CSS
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Creative Commons Attribution 4.0 International
•0•2•8•1•Updated Feb 1, 2025Feb 1, 2025
AnVIL_Book_Getting_Started
Public
A guide for getting started using AnVIL
course genomics guide cloud-computing anvil
CSS
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Creative Commons Attribution 4.0 International
•4•1•10•5•Updated Feb 1, 2025Feb 1, 2025
GDSCN_Book_Statistics_for_Genomics_PCA
Public
A set of lab modules for PCA analysis
course module genomics pca anvil gdscn
CSS
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Creative Commons Attribution 4.0 International
•0•0•1•1•Updated Jan 31, 2025Jan 31, 2025
ottr-docker
Public
Manages dockerfiles and related images available for use with OTTR
edtech-software
Dockerfile
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Creative Commons Zero v1.0 Universal
•0•0•5•1•Updated Jan 30, 2025Jan 30, 2025
GDSCN_Template_Test
Public
CSS
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Creative Commons Attribution 4.0 International
•0•0•4•1•Updated Jan 28, 2025Jan 28, 2025