Introduction to Reproducibility in Cancer Informatics (The Course)
This course introduces the concepts of reproducibility and replicability in the context of cancer informatics. It uses hands-on exercises to demonstrate in practical terms how to increase the reproducibility of data analyses. The course also introduces tools relevant to reproducibility including analysis notebooks, package managers, git and GitHub.
This course will demonstrate how to:
- Understand the fundamental concepts of reproducibility vs replicability.
- Write a basic analysis that could be passed to another person/computer and be re-ran to obtain the same output.
- Write analysis notebook that adheres to best practices for reproducibility and readability.
- Obtain confidence to learn and apply additional reproducibility tools to an analysis.
Quizzes are included in the course to assess learner's comprehension and hands-on activities guide learners in how to apply these concepts to their own analyses.
This course is written for individuals who:
- Have some familiarity with R or Python - have written some scripts.
- Have not had formal training in computational methods.
- Have limited or no familiar with GitHub, Docker, or package management tools
Goal of this course:
Equip learners with reproducibility skills they can apply to their existing analyses scripts and projects. This course opts for an “ease into it” approach. We attempt to give learners doable, incremental steps to increase the reproducibility of their analyses.
What is not the goal:
This course is meant to introduce learners to the reproducibility tools, but it does not necessarily represent the absolute end-all, be-all best practices for the use of these tools. In other words, this course gives a starting point with these tools, but not an ending point. The advanced version of this course is the next step toward incrementally “better practices”.
- 1 Introduction
- 2 Defining reproducibility
- 3 Organizing your project
- 4 Making your project open source with GitHub
- 5 Using Notebooks
- 6 Managing package versions
- 7 Writing durable code
- 8 Documenting analyses
- 9 Code review
- About this Course
- About the Authors
The Leanpub 60-day 100% Happiness Guarantee
Within 60 days of purchase you can get a 100% refund on any Leanpub purchase, in two clicks.
See full terms
80% Royalties. Earn $16 on a $20 book.
We pay 80% royalties. That's not a typo: you earn $16 on a $20 sale. If we sell 5000 non-refunded copies of your book or course for $20, you'll earn $80,000.
(Yes, some authors have already earned much more than that on Leanpub.)
In fact, authors have earnedover $12 millionwriting, publishing and selling on Leanpub.
Learn more about writing on Leanpub
Free Updates. DRM Free.
If you buy a Leanpub book, you get free updates for as long as the author updates the book! Many authors use Leanpub to publish their books in-progress, while they are writing them. All readers get free updates, regardless of when they bought the book or how much they paid (including free).
Most Leanpub books are available in PDF (for computers) and EPUB (for phones, tablets and Kindle). The formats that a book includes are shown at the top right corner of this page.
Finally, Leanpub books don't have any DRM copy-protection nonsense, so you can easily read them on any supported device.