Module-00-Setup
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Introduction to RNA-seq and course setup
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Citation
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Syntax
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Laptop setup instructions
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Prerequisites
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Introduction to AWS
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Logging into Course Compute
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Unix
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Introduction to R
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Environment
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Tool Installation
Module-01-Inputs
Module-02-Alignment
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Introduction to Alignment
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Adapter Trim
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Alignment
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IGV
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Alignment Visualization - Preparation
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Alignment Visualization - IGV
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Alignment Visualization - Allele Expression
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Alignment QC
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Team Assignment - Alignment
Module-03-Expression
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Introduction to Expression Analysis
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Expression Analysis with Stringtie and htseq-count
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Differential Expression with Ballgown
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Differential Expression with edgeR
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Differential Expression with DESeq2
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Compare DE genes across methods
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DE Visualization with Ballgown
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DE Visualization with DESeq2
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DE Visualization Advanced
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DE Pathway Analysis
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Batch Correction - Preparation
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Batch Correction Analysis
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Team Assignment - Expression and DE
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Integrated Assignment
Module-04-Kallisto
Module-05-Isoforms
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Introduction to Isoform Analysis
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Reference Guided Transcript Assembly
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De Novo Transcript Assembly
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Transcript Assembly Merge
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Differential Splicing
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Transcript Assembly Visualization
Module-06-Trinity
Module-07-Trinotate
Module-08-scRNA
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Introduction to Single-cell RNA-seq
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scRNA-seq Data
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Quality Assessment/Clustering
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Cell Type Annotation
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Differential expression analysis
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Gene set enrichment and pathway analysis
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Cancer cell identification
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Differentiation/Trajectory analysis
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TCR/BCR Repertoire Analysis
Module-09-Appendix
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Introduction to the Appendix
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Saving Results
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Abbreviations
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Lectures
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Practical Exercise Solutions
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Team Assignment - Alignment Answers
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Team Assignment - ExpressionDE Answers
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Integrated Assignment Answers
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AWS Setup
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GCP Setup
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POSIT Setup
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Bioinformatics Best Practices
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Complete Result Sets
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Strand Settings
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Log into Compute Canada