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, an R package, a SPARQL endpoint, and a JSON API. 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.

Audience

This course is addressed 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:

Learn how to detect active genes from bulk or single-cell RNA-Seq
Learn what information on expression Bgee can provide
Understand the added value of Bgee data curation and analysis
Learn about Bgee webtools and their utility to research

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)

9:00-9:10 Welcome
9:10-9:40 Overview of Bgee
9:40-9:50 Q&A
9:50-10:35 Present and absent calls from transcriptome data
10:35-10:50 Q&A
10:50-11:05 Break
11:05-11:35 Data integration in Bgee
11:35-11:45 Q&A
11:45-12:15 Bgee tools

Application

The lecture is free of charge, but registration is mandatory .

You will be informed by email of your registration confirmation.

Venue and Time

This course will be streamed for registered participants. The course will start at 9:00 and end at 12:15 CET. Precise information will be provided to the participants on due time.

Additional information

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

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.

Gene Expression made Useful Easily: Tools and Database of Bgee