University Côte d'azur

ECUE Biologie computationnelle des donnees omiques

ECUE's code : SMESVI03

This course belong to UE05 Donnees biologiques en pratique 2 (6 ECTS) which contains 2 ECUE
EUR LIFE
Biochimie et biologie moléculaire , Informatique , Biologie cellulaire
Campus Valrose
Master 2
Semestre impair
Anglais

PRESENTATION

This class is at the crossroads between omics, computer science and statistics. It aims at:

  • developing advanced bioinformatics tools and pipeline
  • exchange with bioinformatics and data science engineers from academic platforms  of the region
  • acquire a basic knowledge of the development tools and techniques now required in all bioinformatics projets: AI, workflow manager, multi-omics...

Course's manager(s)

Marc Bailly-Bechet

In class

  • 8h of lectures
  • 14h of practical work

PREREQUISITES

Before the start of the course, I must ...
  • know omics data analysis tools
  • know omics technologies

OBJECTIVES

By the end of this course, I should be able to...
  • be able to use efficiently a workflow manager (nextflow, galaxy)
  • analyze omics data
  • create reproductible bioinformatics pipelines
  • have a basic knowledge of AI
  • know how to manage bioinformatics tools at the system level (Anaconda, Docker, singularity)
  • analyze multi-omics data

CONTENT

    • Supervised learning
      • Linear regression
      • Logistic regression
      • Decision trees
      • Random forest
    • Unsupervised learning
      • Clustering
      • PCA
    • Manage a bioinformatics analysis:
      • File management and folder organization
      • Versioning and development
      • Management of softwares and scripts
      • Error management
      • Optimizing execution speed
    • Nextflow
      • Introduction to nextflow
      • Docker and nextflow
      • RNA-seq pipeline development
    • Transcriptomics, Proteomics and Single-cell
    • Measuring multiple omics scales
    • Multi omics data integration
      • Visual integration
      • Correlation integration
      • Latent factors integration
      • Overlap integration
  • NGS assembly with Velvet

  • No description
Access to complete Syllabus (Authentification required)
Important
This syllabus has no contractual value. Its content is subject to change throughout this year: be aware to the last updates