Foundations of Data Science

These lessons will help you get your feet in data science and give you tools to help you slice and dice your data into results.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Material

Data Manipulation Olympics

These tutorials take the same dataset, and show you how to slice and dice it in numerous languages

Lesson Slides Hands-on Recordings Input dataset Workflows
Data Manipulation Olympics - JQ
Data Manipulation Olympics - SQL
Data visualisation Olympics - Visualization in R

Bash

These lessons focus on using the Command Line Interface (CLI) and Bash for processing data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Advanced CLI in Galaxy
CLI Educational Game - Bashcrawl
CLI basics

Python

These lessons focus on coding in Python

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Python
Advanced Python
Plotting in Python

Python (Modular)

These lessons cover coding in Python except they attempt to be very modular, having few interdependencies, allowing you to re-arrange or insert them in your existing course curriculum as needed.

Lesson Slides Hands-on Recordings Input dataset Workflows
Python - Math
Python - Functions
Python - Basic Types & Type Conversion
Python - Lists & Strings & Dictionaries
Python - Flow Control
Python - Loops
Python - Files & CSV
Python - Try & Except
Python - Introductory Graduation
Conda Environments For Software Development
Python - Argparse
Python - Testing
Python - Type annotations
Virtual Environments For Software Development
Python - Globbing
Python - Subprocess
Python - Coding Style
Python - Multiprocessing

R

These lessons focus on coding in R

Lesson Slides Hands-on Recordings Input dataset Workflows
R basics in Galaxy
Advanced R in Galaxy
R
dplyr & tidyverse for data processing

SQL

Here you'll learn to use SQL to query databases and extract meaningful results from them.

Lesson Slides Hands-on Recordings Input dataset Workflows
Advanced SQL
Introduction to SQL
SQL Educational Game - Murder Mystery
SQL with Python
SQL with R

Scientific Workflow Management Systems

Here you can find brief tutorials on a couple different workflow engines that you might encounter in the wild.

Lesson Slides Hands-on Recordings Input dataset Workflows
Make & Snakemake

Introduction to Genomics

A data- and galaxy-driven introduction to genomics

Lesson Slides Hands-on Recordings Input dataset Workflows

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Basics of using Git from the Command Line
Variant Calling Workflow
Version Control with Git

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoBérénice Batut avatar Bérénice Batutorcid logoYvan Le Bras avatar Yvan Le Bras

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

orcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosThe Carpentries avatar The CarpentriesAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena Rascheorcid logoLisanna Paladin avatar Lisanna PaladinNU Knight Lab avatar NU Knight Laborcid logoPeter van Heusden avatar Peter van HeusdenBazante Sanders avatar Bazante SandersMaria Christina Maniou avatar Maria Christina ManiouAvans Hogeschool avatar Avans Hogeschoolorcid logoSofoklis Keisaris avatar Sofoklis Keisarisorcid logoSaskia Hiltemann avatar Saskia HiltemannDonny Vrins avatar Donny Vrinsorcid logoBérénice Batut avatar Bérénice Batutorcid logoToby Hodges avatar Toby HodgesTeresa Müller avatar Teresa MüllerMarius van den Beek avatar Marius van den Beek

Funders

This material was funded by:

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar GallantriesBioNT avatar BioNT