Course modules

01 Single Cell Technologies

01 Single Cell Technologies
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01 Single Cell Technologies 113317  
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    01 Single Cell Technologies — 01 The Eukaryotic Single Cell Genomics Facility 01 Single Cell Technologies — 01 The Eukaryotic Single Cell Genomics Facility
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    01 Single Cell Technologies — 02 scRNAseq overview 01 Single Cell Technologies — 02 scRNAseq overview
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    01 Single Cell Technologies — 03 SMARTseq 01 Single Cell Technologies — 03 SMARTseq
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    01 Single Cell Technologies — 04 VDJ-seq 01 Single Cell Technologies — 04 VDJ-seq
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    01 Single Cell Technologies — 05 CITE-seq 01 Single Cell Technologies — 05 CITE-seq
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    01 Single Cell Technologies — 06 Cell Hashing and Multiplexing 01 Single Cell Technologies — 06 Cell Hashing and Multiplexing
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    01 Single Cell Technologies — 07 scATAC-seq 01 Single Cell Technologies — 07 scATAC-seq
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    01 Single Cell Technologies — 08 Conclusion 01 Single Cell Technologies — 08 Conclusion
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02 Quality Control

02 Quality Control
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02 Quality Control 113318  
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    02 Quality Control — 01 Introduction 02 Quality Control — 01 Introduction
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    02 Quality Control — 02 Transcription Bursting 02 Quality Control — 02 Transcription Bursting
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    02 Quality Control — 03 Single Cell Pre-processing 02 Quality Control — 03 Single Cell Pre-processing
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    02 Quality Control — 04 Sequencing Artefacts 02 Quality Control — 04 Sequencing Artefacts
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    02 Quality Control — 05 Spike-in RNAs 02 Quality Control — 05 Spike-in RNAs
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    02 Quality Control — 06 Doublets 02 Quality Control — 06 Doublets
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    02 Quality Control — 07 Filtering 02 Quality Control — 07 Filtering
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    02 Quality Control — 08 Conclusion 02 Quality Control — 08 Conclusion
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03 Normalisation

03 Normalisation
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03 Normalisation 113319  
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    03 Normalisation — 01 Normalisation Methods 03 Normalisation — 01 Normalisation Methods
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    03 Normalisation — 02 Imputation 03 Normalisation — 02 Imputation
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    03 Normalisation — 03 Cell Cycle Scoring 03 Normalisation — 03 Cell Cycle Scoring
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    03 Normalisation — 04 Feature Selection 03 Normalisation — 04 Feature Selection
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    03 Normalisation — 05 Scaling and Regressing Confounders 03 Normalisation — 05 Scaling and Regressing Confounders
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    03 Normalisation — 06 Conclusions 03 Normalisation — 06 Conclusions
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04 Dimensionality Reduction

04 Dimensionality Reduction
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04 Dimensionality Reduction 113320  
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    04 Dimensionality Reduction — 01 Introduction 04 Dimensionality Reduction — 01 Introduction
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    04 Dimensionality Reduction — 02 PCA 04 Dimensionality Reduction — 02 PCA
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    04 Dimensionality Reduction — 03 Graphs 04 Dimensionality Reduction — 03 Graphs
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    04 Dimensionality Reduction — 04 tSNE 04 Dimensionality Reduction — 04 tSNE
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    04 Dimensionality Reduction — 05 UMAP 04 Dimensionality Reduction — 05 UMAP
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    04 Dimensionality Reduction — 06 Conclusion 04 Dimensionality Reduction — 06 Conclusion
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05 Data Integration

05 Data Integration
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05 Data Integration 113321  
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    05 Data Integration — 01 Introduction 05 Data Integration — 01 Introduction
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    05 Data Integration — 02 Linear Integration 05 Data Integration — 02 Linear Integration
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    05 Data Integration — 03 Graph-based Integration 05 Data Integration — 03 Graph-based Integration
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    05 Data Integration — 04 Integration Assessment 05 Data Integration — 04 Integration Assessment
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    05 Data Integration — 05 Summary 05 Data Integration — 05 Summary
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06 Clustering

06 Clustering
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06 Clustering 113322  
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    06 Clustering — 01 Introduction 06 Clustering — 01 Introduction
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    06 Clustering — 02 Hierarchical Clustering 06 Clustering — 02 Hierarchical Clustering
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    06 Clustering — 03 K-means 06 Clustering — 03 K-means
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    06 Clustering — 04 Graphs 06 Clustering — 04 Graphs
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    06 Clustering — 05 Graph Partitioning 06 Clustering — 05 Graph Partitioning
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    06 Clustering — 06 HDBSCAN 06 Clustering — 06 HDBSCAN
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    06 Clustering — 07 Pagoda 06 Clustering — 07 Pagoda
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    06 Clustering — 08 Conclusion 06 Clustering — 08 Conclusion
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07 Differential Expression

07 Differential Expression
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07 Differential Expression 113323  
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    07 Differential Expression — 01 Introduction 07 Differential Expression — 01 Introduction
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    07 Differential Expression — 02 Common Methods 07 Differential Expression — 02 Common Methods
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    07 Differential Expression — 03 Zero-inflated Models 07 Differential Expression — 03 Zero-inflated Models
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    07 Differential Expression — 04 Result Assessment 07 Differential Expression — 04 Result Assessment
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    07 Differential Expression — 05 Method Comparison 07 Differential Expression — 05 Method Comparison
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    07 Differential Expression — 06 Summary 07 Differential Expression — 06 Summary
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08 Gene Set Analysis

08 Gene Set Analysis
Module completed Module in progress Module locked
08 Gene Set Analysis 113324  
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    08 Gene Set Analysis — 01 Introduction 08 Gene Set Analysis — 01 Introduction
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    08 Gene Set Analysis — 02 Gene Sets 08 Gene Set Analysis — 02 Gene Sets
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    08 Gene Set Analysis — 03 Overrepresentation Analysis 08 Gene Set Analysis — 03 Overrepresentation Analysis
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    08 Gene Set Analysis — 04 GSEA 08 Gene Set Analysis — 04 GSEA
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    08 Gene Set Analysis — 05 Summary 08 Gene Set Analysis — 05 Summary
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09 Cell Type Prediction

09 Cell Type Prediction
Module completed Module in progress Module locked
09 Cell Type Prediction 113325  
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    09 Cell Type Prediction — 01 Introduction 09 Cell Type Prediction — 01 Introduction
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    09 Cell Type Prediction — 02 Classifiers Principles 09 Cell Type Prediction — 02 Classifiers Principles
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    09 Cell Type Prediction — 03 KNN Classifier 09 Cell Type Prediction — 03 KNN Classifier
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    09 Cell Type Prediction — 04 SVM Classifier 09 Cell Type Prediction — 04 SVM Classifier
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    09 Cell Type Prediction — 05 Methods Overview 09 Cell Type Prediction — 05 Methods Overview
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    09 Cell Type Prediction — 06 Method Comparison 09 Cell Type Prediction — 06 Method Comparison
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    09 Cell Type Prediction — 07 Hierarchical Progressive Learning 09 Cell Type Prediction — 07 Hierarchical Progressive Learning
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    09 Cell Type Prediction — 08 Summary 09 Cell Type Prediction — 08 Summary
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10 Trajectory Inference

10 Trajectory Inference
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10 Trajectory Inference 113326  
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    10 Trajectory Inference — 01 Introduction 10 Trajectory Inference — 01 Introduction
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    10 Trajectory Inference — 02 ICA 10 Trajectory Inference — 02 ICA
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    10 Trajectory Inference — 03 Diffusion Maps 10 Trajectory Inference — 03 Diffusion Maps
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    10 Trajectory Inference — 04 Minimun Spanning Tree 10 Trajectory Inference — 04 Minimun Spanning Tree
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    10 Trajectory Inference — 05 Graph Abstraction 10 Trajectory Inference — 05 Graph Abstraction
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    10 Trajectory Inference — 06 RNA velocity 10 Trajectory Inference — 06 RNA velocity
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    10 Trajectory Inference — 07 Trajectory Differential Expression 10 Trajectory Inference — 07 Trajectory Differential Expression
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    10 Trajectory Inference — 08 Summary 10 Trajectory Inference — 08 Summary
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11 Spatial Transcriptomics

11 Spatial Transcriptomics
Module completed Module in progress Module locked
11 Spatial Transcriptomics 113327  
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    11 Spatial Transcriptomics — 01 Introduction 11 Spatial Transcriptomics — 01 Introduction
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    11 Spatial Transcriptomics — 02 Spatial Technologies 11 Spatial Transcriptomics — 02 Spatial Technologies
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    11 Spatial Transcriptomics — 03 Analysis of Spatial Data 11 Spatial Transcriptomics — 03 Analysis of Spatial Data
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    11 Spatial Transcriptomics — 04 Spot Deconvolution 11 Spatial Transcriptomics — 04 Spot Deconvolution
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    11 Spatial Transcriptomics — 05 Spatially Aware Analysis 11 Spatial Transcriptomics — 05 Spatially Aware Analysis
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    11 Spatial Transcriptomics — 06 10X Visium 11 Spatial Transcriptomics — 06 10X Visium
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  • Page
    11 Spatial Transcriptomics — 07 Summary 11 Spatial Transcriptomics — 07 Summary
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Pre-course instructions

Pre-course instructions
Module completed Module in progress Module locked
Pre-course instructions 113328  
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    Introduction to Pre-course Introduction to Pre-course
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  • Page
    Knowledge Requirements Knowledge Requirements
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    Zoom Zoom
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  • Page
    Slack Slack
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  • Page
    Conda Conda
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  • Page
    On Mac OS X On Mac OS X
    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
  • Page
    On Ubuntu On Ubuntu
    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
  • Page
    On Windows 10 On Windows 10
    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
  • Page
    On Virtual Box On Virtual Box
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    Create the course conda environment Create the course conda environment
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FAQ

FAQ
Module completed Module in progress Module locked
FAQ 113329  

Schedule

Schedule
Module completed Module in progress Module locked
Schedule 113330  
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    Schedule-2 Schedule-2
    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
  • Page
    Schedule Schedule
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Exercises

Exercises
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Exercises 113331  
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    Exercises Exercises
    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
 
minimum score must view must submit must contribute