5-7 December 2016
9:00 am - 5:00 pm
Instructors: Krzysztof Poterlowicz, Laura Fortunato, Maja Založnik
Helpers: Nadya Fursova, Katy Brown, Hania Pavlou, Aino Jarvelin, Kinga Kamieniarz-Gdula, Michal Gdula
The Biochemistry Department of Oxford University, ELIXIR-UK and the Software Sustainability Institute are proud to organise and host a data carpentry course in data analysis covering introduction to the UNIX shell, GitHub as well as programming and data visualization in R. Standard Software Carpentry workshop will be followed by the third day of hands-on next generation sequencing (NGS) data analysis in R course. Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills 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.
Requirements: Participants must bring a 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). They are also required to abide by Software Carpentry's Code of Conduct.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code during the workshop.
This workshop has been sponsored and supported by:
Please be sure to complete these surveys before and after the workshop.
|09:00||Automating tasks with the Unix shell|
|11:00||Automating tasks with the Unix shell|
|13:30||Version control with Git/Github|
|15:30||Version control with Git/Github|
|16:00||Introduction to R and RStudio|
|17:00||Wrap-up of day 1|
|09:00||Programming in R- Data Structures|
|11:00||Programming in R - Functions explained|
|13:30||Programming in R - Creating Publication-Quality Graphics|
|15:30||Programming in R - Creating Publication-Quality Graphics|
|17:00||Post-workshop questionnaire and wrap-up of day|
|09:00||RNA-seq, ChIP-seq analysis overview|
|10:00||Introduction to the data|
|11:30||Prepartion of read count table|
|12:30||Differential expression analysis with Deseq2|
|14:00||Visualization of RNA-seq results|
|15:30||Relation of gene expression data to ChIP-seq data|
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
See the Git installation video tutorial
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing
bash. There is no need to
Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git.
When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it, try
typing the escape key, followed by
:q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.
nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.
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.