Topic outline

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

    Streamed from Lausanne, 18 June 2021

    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss.

  • Programme

    9:00-12:15 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


    12:15 - 13:15 Lunch break


    13:15-17:15 Hands-on, divided into parallel series (Frédéric Bastian, Marc Robinson-Rechavi, Sara Fonseca and Julien Wollbrett).


    Series 1: Bgee web tools

    • 13:15-14:45 Around the gene page: finding genes, interpreting scores, orthologs and paralogs

    • 14:45-15:00 break

    • 15:00-16:00 Advanced use and interpretation of TopAnat

    • 16:00-16:15 break

    • 16:15-17:00 Download files: expression data and more

    • 17:00-17:15 Final Q&A, conclusion (common with series 2)


    Series 2: Bgee R tools

    • 13:15-13:45 Installing Bgee R packages, simple import and manipulation of data

    • 13:45-15:15 Integrating the BgeeDB package into workflows to use curated data and perform TopAnat computations

    • 15:15-15:30 Break

    • 15:30-17:00 Analysing own RNA-Seq data, bulk or single-cell, with the BgeeCall package and the Bgee Zenodo space

    • 17:00-17:15 Final Q&A, conclusion (common with series 1)