R for Reproducible Scientific Analysis

ELIXIR Italy

Online

Sep 27-30, 2022

2:30 pm - 6:30 pm CEST

Instructors: Silvia Buonaiuto, Vincenza Colonna, Marco Crotti, Gianluca Damaggio, Luca Di Stasio

Helpers: Allegra Via, Loredana Le Pera

Organisers

Allegra Via, National Research Council (CNR) and ELIXIR - Homepage

Loredana Le Pera, Italian National Institute of Heath (ISS) and ELIXIR - Homepage

Vincenza Colonna, National Research Council (CNR) and ELIXIR - Homepage

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

This workshop is only open to people from RENOIR, a European Training Network that aims to develop and implement a PhD programme in the field of muscle regeneration and aging.

Who: The course is aimed at both Bioinformaticians and Biologists who want to learn how to manipulate, process data, and make plots using R. Some best practices for scientific programming will be explained: breakdown analyses into modular units, task automation, and encapsulation. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Sep 27-30, 2022. Add to your Google Calendar.

Requirements: Participants must have access to a computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if there is anything we can do to make this workshop more accessible to you.

Contact: Please email elixir.ita.training@gmail.com or loredanalepera@gmail.com for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

2:30	Welcome & Presentation; Testing setup and zoom; Pre-workshop survey
3:00	Introduction to R and RStudio
4:15	Morning break
4:35	Project Management With RStudio
5:15	Seeking Help
5:45	Data Structures
6:15	Wrap-up

Day 2

2:30	Warm-up
2:45	Data Structures (continued)
4:00	Morning break
4:20	Subsetting Data
6:15	Wrap-up

Day 3

2:30	Warm-up
2:45	Subsetting Data (continued)
3:00	Exploring "gapminder" dataframe
3:30	Control Flow
4:20	Morning break
4:40	Creating Publication-Quality Graphics with ggplot2
6:20	Wrap-up

Day 4

2:30	Warm-up
2:45	Writing Data
3:00	Morning break (I)
3:15	Dataframe Manipulation with dplyr
4:45	Morning break (II)
5:00	Dataframe Manipulation with dplyr (continued)
5:30	Writing Good Software
6:10	Wrap-up; Post-workshop Survey
6:30	END

Setup

To participate in a Software Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Video Tutorial

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.