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- Supervised learning
- Linear regression
- Logistic regression
- Decision trees
- Random forest
- Unsupervised learning
- Clustering
- PCA
ECUE Biologie computationnelle des donnees omiques
Code de l'ECUE : SMESVI03
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...
Responsable(s) du cours
Marc Bailly-Bechet
Présentiel
- 8h de cours magistral
- 14h de travaux pratiques
PREREQUIS
Avant le début du cours, je dois ...
-
know omics data analysis tools
-
know omics technologies
OBJECTIFS
A la fin de ce cours, je devrais être capable de...
- 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
CONTENU
-
Introduction to AI (Machine learning)
-
Bioinformatic workflow development with Nextflow
- 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
- Manage a bioinformatics analysis:
-
Multi-omics analysis
- Transcriptomics, Proteomics and Single-cell
- Measuring multiple omics scales
- Multi omics data integration
- Visual integration
- Correlation integration
- Latent factors integration
- Overlap integration
-
RNA-seq transcriptome assembly
NGS assembly with Velvet
-
RNA-seq data analysis with R
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