Gene expression made useful easily: tools and database of Bgee (lectures)

Overview

This is a course on bioinformatics resources taught by the developers of the resources. Bgee is a curated database of gene expression in animals, including model species such as human, mouse or drosophila, and others such as livestock, primates, or fishes. Bgee integrates information from single-cell and bulk RNA-seq, microarrays, and in situ hybridization. These data are available through a web interface and an R package. Bgee also includes tools which use these data, such as TopAnat or Expression Comparison, and allows integration with users' own data through another R package. In this course, we will present the curated and pre-analysed gene expression data in Bgee. Hands-on will be open to make use of the Bgee companion tools, Bgee’s online functionalities, or Bgee R packages to retrieve data and integrate them into one’s own workflow (e.g. RNA-seq analysis R script).

Audience

This course is targeted to life scientists who need to retrieve curated gene expression, obtain expression-based knowledge on genes of interest, or compare expression between genes and between species.

Learning outcomes

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

• Distinguish types of expression data and the added value of curation, annotation, and consistent analysis.
• Explain the steps of gene expression analysis.
• Retrieve precomputed gene expression data through the web.

Prerequisites

Technical

This course will be streamed, you are thus required to have your own computer with an internet connection.

Schedule - CET time zone

9:00-12:15 CET time zone - Online lectures (Frédéric Bastian and Marc Robinson-Rechavi)

• 9:00-9:15 Welcome
• 9:15-10:00 Overview of Bgee
• 10.00-10:15 Questions and answers
• 10:15-11:00 Manipulating integrated data
• 11:00-11:15 Questions and answers
• 11:15-12:00 Manipulating processed data
• 12:00-12:15 Questions and answers

Application

Attendance to lectures are free-of-charge, however registration is mandatory. Deadline for registration is set to 04/06/2021.

You will be informed by email of your registration confirmation.

If you are interested to attend the lectures and practicals, apply here

Venue and Time

This course will be streamed for registered participants.

The lectures will start at 9:00 and end around 12:15 CET. Precise information will be provided to the participants on due time.

Additional information

Coordination: Valeria Di Cola (valeria.dicola@sib.swiss)

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.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

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