R for Reproducible Scientific Analysis

ELIXIR Italy

Online

Jul 14-17, 2020

9:00 am - 13:00 pm

Instructors: Vincenza Colonna, Loredana Le Pera, Allegra Via

Helpers: Silvia Buonaiuto, Gianluca Damaggio, Marco Pietrosanto

Organisers

Allegra Via, National Research Council and ELIXIR - Homepage

Loredana Le Pera, National Research Council and ELIXIR - Homepage

Vincenza Colonna, National Research Council and ELIXIR - Homepage

Registration

Here is the registration link.

Deadline for application is: Jul 1, 2020.

A maximum of 15 candidates will be selected on the basis of motivations given in the application form.

Selected participants will be notified by Jul 7, 2020.

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".

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: Jul 14-17, 2020. Add to your Google Calendar.

Requirements: Participants must have a desktop/laptop 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 you require any accommodations or 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.


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

09:00 Welcome & Presentation; Testing setup and zoom; Pre-workshop survey
10:00 Introduction to R and RStudio
11:00 Project Management With RStudio
11:30 Morning break
11:50 Seeking Help
12:10 Data Structures
13:10 Wrap-up

Day 2

09:00 Warm-up
09:15 Exploring Data Frames
09:45 Subsetting Data
10:45 Morning break
11:05 Control Flow
12:10 Creating Publication-Quality Graphics with ggplot2
13:10 Wrap-up

Day 3

09:00 Warm-up
09:15 Vectorization
09:40 Functions Explained
10:40 Morning break
11:00 Writing Data
11:20 Splitting and Combining Data Frames with plyr
12:20 Dataframe Manipulation with dplyr
13:10 Wrap-up

Day 4

09:00 Warm-up
09:15 Dataframe Manipulation with dplyr (Continued)
09:30 Dataframe Manipulation with tidyr
10:15 Producing Reports With knitr
11:30 Morning break
11:50 Producing Reports With knitr (Continued)
12:10 Writing Good Software
12:30 Wrap-up; Post-workshop Survey
13:10 END

Syllabus


Setup

To participate in a Software Carpentry workshop, you will need access to the software 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.

R

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

Video Tutorial

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.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.