Functional genomic data analysis : transcriptomics
Master in Life Science, ENS
UNBIO1-067 | Functional genomic data analysis : transcriptomics
Level | Semester : M2 | S1
Where : ENS Biology Department, 3rd floor
Duration : 1 week | 30 hours (including personal work)
Dates : September 8-12, 2025
Hours : 09:30-12:30 | 13:30-17:00
Maximum class size : 30 students
—2024-2025 program—
Coordination
Stéphane Le Crom, Sorbonne Université
Lucie Gaspard Boulinc, École normale supérieure, Paris
Léa Swales, École normale supérieure, Paris
Credits
3 ECTS
Keywords
Functional Genomics | Transcriptomics | High Throughput Sequencing | Microarrays | Bioinformatics.
Course Prerequisites
Computer knowledge : bases in computer programming, practice of Linux command lines and knowledge of R language.
Competency level in Unix : Advanced exploration of the file system, and workspace
Course objectives and description
Aims : The aims of this teaching unit are to understand and handle various data format that are available from high throughput sequencing techniques in genomics. This course allows students to better appreciate the limits and drawbacks of high throughput genomics datasets.
Themes : This course introduces the high throughput sequencing techniques and the various applications available in genomics. It focuses on the analysis of gene expression studies and covers the most important bioinformatics and statistical concepts to delineate differentially expressed genes.
Computer-training sessions make use of open source software like R programming language, MeV (MultiExperiment Viewer) and IGV (Integrative Genomics Viewer).
The course covers the following fields : data quality analysis, read mapping on a reference genome, read alignment visualization, data normalization, statistical differential analysis, functional annotation and expression network visualization.
Organization : The course is organized over one week, with classes during the morning, computer-training sessions during the afternoon and free analysis workshop around datasets.
Assessment
Students will be evaluated based on a written report at the end of the week.
Course material
The practicals will be conducted on the core cluster of the Institut Français de Bioinformatique. We kindly acknowledge the IFB for supporting this course.
During this course, you will learn some competencies in Unix from levels U5 and U7 (see Competency matrix in unix in bioinformatics)
Teaching team
Stéphane Le Crom (Sorbonne Université, Paris)
Lucie Gaspard Boulinc (École normale supérieure, Paris)
