Gene expression made useful easily: tools and database of Bgee

Date 27 April 2020
Speaker(s) Frédéric Bastian, Marc Robinson-Rechavi and others
ECTS 0.25
Fees *academic: 60 CHF   -   for-profit: 300 CHF
Cancellation deadline 13 Apr 2020
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

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 primates or fishes. 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 allow integration with users own data.

In this course, we will present the curated and pre-analysed gene expression data in Bgee. We will also make use of the Bgee companion tools, Bgee’s online functionalities, and Bgee R packages to retrieve data and integrate them into one’s own workflow (e.g. RNA-seq analysis R script).

Learning objectives

After the course, participants should be able 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.
  • Obtain expert knowledge of the online tools of Bgee (run analyses knowing which options to use, what are the consequences of choices of data to put in, what is more or less reliable or powerful).
  • Apply the Bgee R tools and their integration into own workflows.
  • Analyse data from species or conditions absent from Bgee
  • Interpret biological results obtained with Bgee and associated tools.

Prerequisites

Knowledge / competencies

Basic knowledge of R is required for some exercises.

Technical

You are required to bring your own laptop with an internet connection.

Venue and Time

University of Lausanne, Amphipôle building, classroom 340 (Metro M1 line, Sorge station).

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

Application

The registration fees for academics are 60 CHF, and 300 CHF for participants from private companies. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set is set to 13/04/2020. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

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

Additional information

Coordination: Patricia Palagi

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.

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