Gene Expression made Useful Easily: Tools and Database of Bgee

All those signing up for this course will be accepted and will receive the Zoom link to connect a few days before the course starts.

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:

• Detect active genes from bulk or single-cell RNA-Seq
• Describe information on expression that Bgee can provide
• Recognise the added value of Bgee data curation and analysis
• Highlight the 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: Patricia Palagi, SIB Training Group

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