Course modules

Preparation

Preparation
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Preparation 112481  
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    Overview Overview
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    Pre-course Pre-course
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    Data pre-processing Data pre-processing
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Day 1: Introduction, ML view of omics integration, introduction to Unsupervised Integration

Day 1: Introduction, ML view of omics integration, introduction to Unsupervised Integration
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Day 1: Introduction, ML view of omics integration, introduction to Unsupervised Integration 112482  
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    Introduction Introduction
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    Machine Learning view of Integration Machine Learning view of Integration
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    Unsupervised Integration Unsupervised Integration
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    Lab: Unsupervised Integration through MOFA2 Lab: Unsupervised Integration through MOFA2
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Day 1: Unsupervised Integration through MOFA

Day 1: Unsupervised Integration through MOFA
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Day 1: Unsupervised Integration through MOFA 112483  
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    Multi-Omics Factor Analysis - MOFA Multi-Omics Factor Analysis - MOFA
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    Lab: MOFA for personalized medicine Lab: MOFA for personalized medicine
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    Bonus materials: mofa Bonus materials: mofa
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Day 2: Supervised Integration through Mixomics

Day 2: Supervised Integration through Mixomics
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Day 2: Supervised Integration through Mixomics 112484  
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    Your instructor Your instructor
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    Preliminary background on PCA Preliminary background on PCA
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    Lecture Lecture
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    Lab: Application to a microarray data set Lab: Application to a microarray data set
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    Bonus materials: mixomics Bonus materials: mixomics
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Day 2: Deep Learning and UMAP integration

Day 2: Deep Learning and UMAP integration
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Day 2: Deep Learning and UMAP integration 112485  
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    Deep Learning for Omics integration Deep Learning for Omics integration
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    Lab: Deep learning Lab: Deep learning
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    UMAP for data integration UMAP for data integration
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    Lab: UMAP for data integration Lab: UMAP for data integration
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    Bonus lab: dimensionality reduction Bonus lab: dimensionality reduction
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    Bonus lab: integration at single-cell level Bonus lab: integration at single-cell level
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    Bonus materials: deep learning Bonus materials: deep learning
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Day 3: Network Analysis

Day 3: Network Analysis
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Day 3: Network Analysis 112486  
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    Introduction to network analysis Introduction to network analysis
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    Network inference and properties Network inference and properties
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    Community analysis Community analysis
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    Lab: Network construction and analysis of a transcriptomic and metabolomic dataset Lab: Network construction and analysis of a transcriptomic and metabolomic dataset
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    Bonus lab: Feature selection Bonus lab: Feature selection
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    Bonus lab: data pre-processing in python Bonus lab: data pre-processing in python
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Day 4: Similarity Network Fusion and Non-negative Matrix Factorization

Day 4: Similarity Network Fusion and Non-negative Matrix Factorization
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Day 4: Similarity Network Fusion and Non-negative Matrix Factorization 112487  
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    Non-negative Matrix Factorization Non-negative Matrix Factorization
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    Similarity Network Fusion Similarity Network Fusion
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    Lab: Non-negative Matrix Factorization Lab: Non-negative Matrix Factorization
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    Lab: Similarity Network Fusion Lab: Similarity Network Fusion
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    Bonus material: NMF and SNF Bonus material: NMF and SNF
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Day 4: Genome-scale metabolic modeling

Day 4: Genome-scale metabolic modeling
Module completed Module in progress Module locked
Day 4: Genome-scale metabolic modeling 112488  
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    Constraint-based modeling of metabolism Constraint-based modeling of metabolism
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    Lab: constraint-based modeling of metabolism (in Python with cobrapy) Lab: constraint-based modeling of metabolism (in Python with cobrapy)
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Day 5: Gene set analysis, reporter features and network-meta analysis

Day 5: Gene set analysis, reporter features and network-meta analysis
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Day 5: Gene set analysis, reporter features and network-meta analysis 112489  
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    Network meta-analysis - Lecture Network meta-analysis - Lecture
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    Network meta-analysis - lab Network meta-analysis - lab
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    Gene set analyses - Lecture Gene set analyses - Lecture
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    Gene set analysis and reporter features - lab Gene set analysis and reporter features - lab
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Bonus material

Bonus material
Module completed Module in progress Module locked
Bonus material 112490  
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    Multi Omics Data Management Multi Omics Data Management
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    Visualization with Cytoscape Visualization with Cytoscape
    Score at least   Must score at least   to complete this module item Scored at least   Module item has been completed by scoring at least   View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark completed Must mark this module item done in order to complete Marked completed Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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    Circos & Hive visualization Circos & Hive visualization
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Additional Materials

Additional Materials
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Additional Materials 112491  
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    Additional reading Additional reading
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    Invited lectures Invited lectures
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    FAQs FAQs
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minimum score must view must submit must contribute