General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. 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 "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. 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: Jan 31-Feb 4, 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 you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email renato.alves@embl.de or lisanna.paladin@embl.de for more information.

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

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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.

Report a Code of Conduct Incident

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Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

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Surveys

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

Pre-workshop Survey

Post-workshop Survey

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Schedule

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Setup

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

This workshop is designed to be run on your laptop. First, you will need to download the data we use in the workshop. Then, you need to install some software. After following the instructions on this page, you should have everything you need to participate fully in the workshop!

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 learing 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.

Data

You can download all of the data used in this workshop by clicking this download link. The file is 38.4 MB.

Clicking the download link will automatically download all of the files to your default download directory as a single compressed (.zip) file. To expand this file, double click the folder icon in your file navigator application (for Macs, this is the Finder application).

For a full description of the data used in this workshop see the data page.

Software

Software	Install	Manual	Available for	Description
Spreadsheet program	Link	Link	Linux, MacOS, Windows	Spreadsheet program for organizing tabular data.
OpenRefine	Link	Link	Linux, MacOS, Windows	Program for reproducibly cleaning data.
R	See install instructions below.		Linux, MacOS, Windows	Programming language for data analysis and visualisation.
RStudio	Link	Cheatsheet	Linux, MacOS, Windows	Integrated development environment for R.

Spreadsheet program

• To interact with spreadsheets, we can use LibreOffice, Microsoft Excel, Gnumeric, OpenOffice.org, or other programs. Commands may differ a bit between programs, but the general ideas for thinking about spreadsheets are the same. For this workshop, we recommend using either Microsoft Excel (paid software) or LibreOffice (free and open source). Other spreadsheet programs may not have all of the features we will be exploring in this workshop.

• To install LibreOffice, go to their download page. The website should automatically select the correct option for your operating system. Click the “Download” button. You will go to a page that asks about a donation, but you don’t need to make one. Your download should begin automatically. Once the installer is downloaded, double click on it (you may need to open your Downloads folder) and LibreOffice should install.

OpenRefine

• OpenRefine is a Java program that runs on your local machine (not on the cloud). Although it displays in your browser, no web connection is needed and your data remains local. You need to have a ‘Java Runtime Environment’ (JRE) installed on your computer to run OpenRefine. If you don’t already have one installed then you can download and install from http://java.com by going to the site and clicking “Free Java Download”.

• To install OpenRefine, go to their download page. From the download page, select either “Windows kit”, “Mac kit”, or “Linux kit” - depending on your operating system - and follow the instructions next to your download link. This lesson has been tested with all versions of OpenRefine up to the latest tested version, 3.2. If you are using an older version, it is recommended you upgrade to the latest tested version. After installing, you can delete the installer .dmg file.

• You may get an error message: “OpenRefine.app can’t be opened because it is from an unidentified developer.” If you get this message, open your system preferences and click “Security & Privacy”. You will see a message “OpenRefine.app was blocked from opening because it is from an unidentified developer.” Click “Open Anyway” and “Yes”. OpenRefine should open in your default web browser.

• OpenRefine does not support Internet Explorer or Edge. Please use Firefox, Chrome or Safari instead.

R and RStudio

• R and RStudio are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. You need to install R before you install RStudio. After installing both programs, you will need to install some specific R packages within RStudio. Follow the instructions below for your operating system, and then follow the instructions to install tidyverse and other packages.

Windows

If you already have R and RStudio installed

• Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.

• To check which version of R you are using, start RStudio and the first thing that appears in the console indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.

• Follow the steps in the instructions for everyone at the bottom of this page.

If you don’t have R and RStudio installed

• Download R from the CRAN website.
• Run the .exe file that was just downloaded
• Go to the RStudio download page
• Under Installers select RStudio x.yy.zzz - Windows Vista/7/8/10 (where x, y, and z represent version numbers)
• Double click the file to install it

• Once it’s installed, open RStudio to make sure it works and you don’t get any error messages

• Follow the steps in the instructions for everyone at the bottom of this page.

macOS

If you already have R and RStudio installed

• Open RStudio, and click on “Help” > “Check for updates”. If a new version is available, quit RStudio, and download the latest version for RStudio.
  • To check the version of R you are using, start RStudio and the first thing that appears on the terminal indicates the version of R you are running. Alternatively, you can type sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it.
• Follow the steps in the instructions for everyone at the bottom of this page.

If you don’t have R and RStudio installed

• Download R from the CRAN website.
• Select the .pkg file for the latest R version
• Double click on the downloaded file to install R
• It is also a good idea to install XQuartz (needed by some packages)
• Go to the RStudio download page
• Under Installers select RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit) (where x, y, and z represent version numbers)
• Double click the file to install RStudio

• Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.

• Follow the steps in the instructions for everyone at the bottom of this page.

Linux

• Follow the instructions for your distribution from CRAN, they provide information to get the most recent version of R for common distributions. For most distributions, you could use your package manager (e.g., for Debian/Ubuntu run sudo apt-get install r-base, and for Fedora sudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 3.5.1.
• Go to the RStudio download page
• Under Installers select the version that matches your distribution, and install it with your preferred method (e.g., with Debian/Ubuntu sudo dpkg -i rstudio-x.yy.zzz-amd64.deb at the terminal).
• Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.
• Follow the steps in the instructions for everyone

For everyone

• After installing R and RStudio, you need to install a few packages. Start RStudio by double-clicking the icon and then type: install.packages(c("tidyverse", "corrplot", "corrr", "hexbin", "patchwork", "ggfortify", "broom", "RSQLite", "BiocManager")). You can also do this by going to Tools -> Install Packages and typing the names of the packages you want to install, separated by a comma. Finally, install ComplexHeatmap from BioConductor using: BiocManager::install("ComplexHeatmap")