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.

Material

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

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
cyoa
Data visualisation Olympics - Visualization in R
cyoa R rmarkdown-notebook jupyter-notebook
Data Manipulation Olympics - SQL
cyoa sql jupyter-notebook
Data Manipulation Olympics - JQ
cyoa json

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
bash jupyter-notebook
CLI Educational Game - Bashcrawl
game bash jupyter-notebook
CLI basics
bash jupyter-notebook

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
conda jupyter-notebook
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
interactive-tools R
Advanced R in Galaxy
R
dplyr & tidyverse for data processing
R rmarkdown-notebook jupyter-notebook

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
SQL jupyter-notebook
Introduction to SQL
SQL jupyter-notebook
SQL Educational Game - Murder Mystery
game SQL jupyter-notebook
SQL with Python
SQL Python jupyter-notebook
SQL with R
SQL R rmarkdown-notebook jupyter-notebook

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
One protein along the UniProt page
Variant Calling Workflow
Version Control with Git

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.

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Editorial Board

This material is reviewed by our Editorial Board:

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

Contributors

This material was contributed to by:

orcid logoSimon Gladman avatar Simon Gladman orcid logoCristóbal Gallardo avatar Cristóbal Gallardo Teresa Müller avatar Teresa Müller Bazante Sanders avatar Bazante Sanders orcid logoHelena Rasche avatar Helena Rasche Anton Nekrutenko avatar Anton Nekrutenko Maria Christina Maniou avatar Maria Christina Maniou Marius van den Beek avatar Marius van den Beek Yongbin Li avatar Yongbin Li orcid logoAnthony Bretaudeau avatar Anthony Bretaudeau NU Knight Lab avatar NU Knight Lab orcid logoSofoklis Keisaris avatar Sofoklis Keisaris orcid logoLisanna Paladin avatar Lisanna Paladin Mateusz Kuzak avatar Mateusz Kuzak orcid logoWendi Bacon avatar Wendi Bacon orcid logoSaskia Hiltemann avatar Saskia Hiltemann orcid logoBeatriz Serrano-Solano avatar Beatriz Serrano-Solano orcid logoMartin Čech avatar Martin Čech orcid logoToby Hodges avatar Toby Hodges Donny Vrins avatar Donny Vrins orcid logoBjörn Grüning avatar Björn Grüning orcid logoPeter van Heusden avatar Peter van Heusden orcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulos orcid logoNate Coraor avatar Nate Coraor orcid logoBérénice Batut avatar Bérénice Batut

Funding

These individuals or organisations provided funding support for the development of this resource

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BioNT
Co-funded by the European Union
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The Carpentries
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
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