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

Explore more trainings from the Innovation Lab for Crop Improvement

Software Interoperability on the ILCI JupyterHub

Discover software programs available in the ILCI JupyterHub and how big data can be directly accessed for computation without the need to download and upload these large files.

Quantitative genetics

Learn basic quantitative genetics concepts and basic statistical methods for genetic data analysis with a focus on genomic selection

GoHy

Discover more about the goal-directed hypothesis-driven applied scientific method