ELIXIR-SIB Data Carpentry with R - Genomics curriculum

We are sorry but this course is oversubscribed, with a long waiting list. Keep an eye in our distribution list (sign in here) for the announcements of future courses.

ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559

Overview

This workshop is hosted by the SIB Swiss Institute of Bioinformatics and the Statistical Bioinformatics Group (Institute of Molecular Life Sciences at the University of Zurich).

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.

We will cover Data organization in spreadsheets; Introduction to command line; Introduction to R; Data analysis in R, Data visualization in R and additional topics. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.

Audience

This course is addressed to graduate students and other researchers with little to no R experience.

Learning objectives

At the end of the course, the participants are expected to:

• Learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database.
• Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.
• Use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation.

Prerequisites

Knowledge / competencies

This course is designed for beginners and there is no programming requirement.

Technical

Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on.

This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. With the exception of a spreadsheet program all of the software and data used in the workshop are hosted on an Amazon Machine Image (AMI).

Instances will be set up for you and your instructor will supply the ip_address and password that you need to login. You will need an SSH client to connect to the instances.

Please, make sure that you have the following:

• Spreadsheet program such as Excel, or free LibreOffice.
• SSH client. On a Mac or Linux machine, you can access it through a program called Terminal, which is already available on your computer. If you’re using Windows, you’ll need to download a separate program to access the cloud instance, such as PuTTY.
• An up to date browser

Schedule

Application

We are sorry but this course is oversubscribed, with a long waiting list.

This course is free of charges. It is sponsored by ELIXIR-EXCELERATE.

Deadline for registration and cancellation is set to 03/06/2019. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

Room Y55-L-06/08 University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland

The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants on due time.

Additional information

Coordination: Patricia Palagi

A certificate of attendance will be delivered to the participants attending the workshop in full.

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.

Participants are required to abide by Data Carpentry's Code of Conduct.