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<!--Delete this section below upon using the template-->

## Open-source Tools for Training Resources - OTTR
## Tools for Reproducible Workflows

Go to [ottrproject.org](https://www.ottrproject.org/) to get started! :tada:

The purpose of this course template and guide is to make course publishing maintenance across multiple different platforms _less painful_.

_This template and guide helps you_:

- Edit and write a course in [RMarkdown files](https://rmarkdown.rstudio.com/) and have it published to multiple different platforms:
- [Leanpub](https://leanpub.com/bookstore?type=course)
- [Bookdown](https://bookdown.org/)
- [Coursera](https://www.coursera.org/)
- Have [Github action robots](https://www.ottrproject.org/customize-robots.html) do your repetitive tasks like spell check and re-rendering.
- Use [automagic conversion](https://github.com/jhudsl/ottrpal) to ease the lift of prepping the material for different platforms' formats.
- Use [our Docker image](https://hub.docker.com/repository/docker/jhudsl/base_ottr) for consistency across authors as well as to help you [avoid dependency hell](https://en.wikipedia.org/wiki/Dependency_hell).

[See the OTTR pre-print here!](https://arxiv.org/abs/2203.07083)

<img src="https://docs.google.com/presentation/d/18k_QN7l6zqZQXoiRfKWzcYFXNXJJEo6j4daYGoc3UcU/export/png?id=18k_QN7l6zqZQXoiRfKWzcYFXNXJJEo6j4daYGoc3UcU&pageid=gf4fcf6569c_2_29" width="500"/>

## Courses that have been made using this template:
- [Documentation and Usability](https://jhudatascience.org/Documentation_and_Usability/)
- [Leadership for Cancer Informatics Research](https://jhudatascience.org/Informatics_Research_Leadership/)
- [Reproducibility in Cancer Informatics](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/)
- [Advanced Reproducibility in Cancer Informatics](https://jhudatascience.org/Adv_Reproducibility_in_Cancer_Informatics/)

## To Get Started
- Go to the [ottrproject.org](https://www.ottrproject.org/).
- Check out the [rendered version of the template](https://jhudatascience.org/OTTR_Template/).
- Please take a look at the [code of conduct](./code_of_conduct.md).
- If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated.

<!--Delete everything above this line upon using the template-->

# {Course Name}

[![Render Bookdown and Coursera](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-all.yml/badge.svg)](https://github.com/jhudsl/OTTR_Template/actions/workflows/render-all.yml)

This course was created from [this GitHub template](https://github.com/jhudsl/OTTR_Template).

You can see the rendered course material here: {Link to rendered bookdown and/or to the Leanpub.}

If you would like to contribute to this course material, take a look at the [getting started GitHub wiki pages](https://github.com/jhudsl/OTTR_Template/wiki).

## About this course

This course introduces {info on what this course introduces}
This is the GitHub repository for the Tools for Reproducible Workflows course. This course explores a variety of tools that can assist with reproducible data analysis from a broad range of fields. This course was funded as part of a series of courses in the [Training Module for Reproducible Data Science Research project](https://reporter.nih.gov/search/k_pXzn8wfUeEvaWpnzIToA/project-details/10663171).

## Learning Objectives

This course will teach learners to:
This course will demonstrate how to:

1. Explain best practices for making analyses more reproducible and transparent
2. Use special features in RStudio for efficiency and reproducibility
3. Configure and organize projects for data analysis using the here package and the ProjectTemplate package
4. Create reproducible reports using RMarkdown and Quarto
5. Write custom functions for reuse of code
6. Test functions with the testthat package
7. Setup and use Git and GitHub to track changes over time 8. Share data and code publicly

- {You can use https://www.bobpikegroup.com/trainer-blog/5-steps-to-writing-clear-and-measurable-learning-objectives to define some learning objectives here}
- {More learning objectives}

## Encountering problems?
This course was built with [OTTR](https://www.ottrproject.org/)

If you are encountering any problems with this course, please file a GitHub issue or contact us at {Some email or web address with a contact form}.

<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />All materials in this course are licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a> unless noted otherwise.
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