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This course is intended to provide the students with the prerequisites needed to be able to follow the courses of the Bioinformatics track dedicated to the analysis of NGS data (B4, B5, B6, B7, B8, B9, B10, B11).

The course has three main parts:
1 - Main UNIX commands
2 - Main R commands / getting acquainted with R scripts and Rstudio
3 - Main Galaxy commands

Teacher: Victoire BAILLET
Teacher: Blaise LI

B4 - Basic concepts in HTS data analysis

Objectives:

Understand the key concepts underlying the quantification and comparison of OMIC datasets
Perform the initial steps of most HTS data analysis

Teacher: Victoire BAILLET
Teacher: Claudia CHICA

B5 - Expression, quantification, differential analysis

Objectives:

Design a successful transcriptomics experiment
How to get differential expressed genes from raw data

Teacher: Elise JACQUEMET
Teacher: Emmanuelle PERMAL

B6 - Variant Calling

Objectives:

Learn the key steps to obtain genetic reliable variants from raw sequencing reads
First applications : use filtered files of variants to perform basic analyses

Teacher: Pascal CAMPAGNE
Teacher: Adrien PAIN

B7 - Genotype data & association studies

Objectives:

Getting exposed to important applications in the analysis of genetic data, genomewide
Analysing genomic data with R and other popular software

Teacher: Vincent LAVILLE
Teacher: Amaury VAYSSE

B8 - ChIP-seq data analysis

Objective:

Be able to analyze ChIP-seq data from sequencing reads to functional interpretation

B9 - Single cell data analysis

Objectives:

Get acquainted with the key concepts of scRNAseq raw data analysis, quantification, functional characterization and visualization.

Teacher: Claudia CHICA
Teacher: Stephan FISCHER
Teacher: Bernd JAGLA
Teacher: Yann LOE MIE
Teacher: Sébastien MELLA
Teacher: Olivier MIRABEAU

B10 - Functional analysis

Objectives

Understand the key concepts of functional analysis
Perform functional analysis on RNA-Seq data on a simple design using R tools

Teacher: Eli BARTHOME
Teacher: Natalia PIETROSEMOLI

B11 - Metagenomics

Teacher: Amine GHOZLANE

B12- Advanced Unix commands

Objectives:

understand more complex but useful options and commands
learn regular expressions and few commands using them,
everything needed to create your firsts own scripts.

IA9 - session 7: Tracking cells in very large images with Mastodon

Using TrackMate for analysis of time-lapse microscopy movies.

This course is aimed at beginners in bioimage analysis, that wants to learn how to analyse time-lapse movies. Such movies can follow the movement of cells, in 2D or 3D over time, or the motility of organelles and large objects. They offer unique insight into the dynamics of biology objects, on the evolution of their morphology and of molecular processes, imaged via transmission light or fluorescence microscopy.

This half a day course includes a brief theoretical introduction about tracking algorithms, and is followed by a hands-on tutorial. For the tutorial we will use TrackMate (https://imagej.net/plugins/trackmate/), which is a somewhat popular Fiji plugin for tracking, developed in the Image Analysis Hub.

What do you need to attend:

Your laptop, Mac or PC
A mouse (mandatory)
Fiji installed (https://fiji.sc)
The following tutorial materials: https://dl.pasteur.fr/fop/ybFP2XYA/TrackMateTutorialMaterial.zip

For more information contact Jean-Yves.

Teacher: Jean-Yves TINEVEZ

IA8 - session 7: Tracking cells and organelles with TrackMate

Using TrackMate for analysis of time-lapse microscopy movies.

This course is aimed at beginners in bioimage analysis, that wants to learn how to analyse time-lapse movies. Such movies can follow the movement of cells, in 2D or 3D over time, or the motility of organelles and large objects. They offer unique insight into the dynamics of biology objects, on the evolution of their morphology and of molecular processes, imaged via transmission light or fluorescence microscopy.

This half a day course includes a brief theoretical introduction about tracking algorithms, and is followed by a hands-on tutorial. For the tutorial we will use TrackMate (https://imagej.net/plugins/trackmate/), which is a somewhat popular Fiji plugin for tracking, developed in the Image Analysis Hub.