Online workshop

Introduction to JupyterHub

About the course

The JupyterHub workshop hosted by the Feed the Future Innovation Lab for Crop Improvement introduces beginners to the use of a cloud-based interactive coding and documentation environment for data analysis projects. This page is a static hub that provides documentation from that workshop as a resource or for people who missed the live sessions. We aim to provide researchers in plant breeding disciplines with the skills necessary to operate R within JupyterHub.

Session 1: Getting Started

Topics: Logging in, navigating directories, creating a directory, creating a notebook, notebook cells, Markdown syntax.

Learning resource: More Markdown syntax

Logging in and creating a notebook 7:44

Session 1.1 exercises

What are notebook cells? 4:55

Session 1.2 exercises

Markdown Basics 9:10

Session 1.3 exercises

Session 2: Using Base R in Jupyter Notebooks

Topics: Using R within a Jupyter Notebook and an Introduction to base R coding, including: base functions, reading in data, manipulating data, generating summary statistics, plotting and visualizing data.

The Basics of R Part 1 13:03

Session 2.1 exercises

The Basics of R, Part 2 11:38

Session 2.2 exercises

Session 3: More R Basics and importing, exporting, and sharing

Topics: Data manipulation in R, R packages, importing and exporting data and figures, sharing notebooks

The Basics of R, Part 3 25:31

Session 3.1 exercises

Importing and Exporting in Jupyter  24:51

Session 3.2 exercises

Course facilitators

Bethany Econopouly

International Applied Genomics Lead

Brandon Monier

Postdoc, Genomics

Terry Casstevens

Programmer Analyst, Genomics

Francisco Francisco Agosto-Perez

Software developer, Breeding informatics

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