2016 CSHL Course - Plant Sciences
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    • RNA-Seq
    • Overview
      • Background
      • Requirements
    • Slides
      • Slides
    • Introduction to R
      • 1. Overview
      • 2. R Package Repositories
      • 3. Installation of R and Add-on Packages
      • 4. Getting Around
      • 5. Basic Syntax
      • 6. Data Types
      • 7. Data objects
      • 8. Important Utilities
      • 9. Operators and Calculations
      • 10. Reading and Writing External Data
      • 11. Useful R Functions
      • 12. SQLite Databases
      • 13. R Markdown
      • 14. Session Info
      • 15. References
    • R Graphics
      • 1. Overview
      • 2. Base Graphics
      • 3. Grid Graphics
      • 4. lattice Graphics
      • 5. ggplot2 Graphics
      • 6. Specialty Graphics
      • 7. Genome Graphics
      • 8. References
    • NGS Workflow Overview
      • 1. Background
      • 2. Getting Started
      • 3. More detail
      • 4. Workflow demo
      • 5. Version information
      • 6. References
    • RNA-Seq Workflow
      • 1. Introduction
      • 2. Sample definitions and environment settings
      • 3. Read preprocessing
      • 4. Alignments
      • 5. Read distribution across genomic features
      • 6. Read quantification per annotation range
      • 7. Analysis of differentially expressed genes with edgeR
      • 8. GO term enrichment analysis of DEGs
      • 9. Clustering and heat maps
      • 10. Render report in HTML and PDF format
      • 11. Version Information
      • 12. Funding
      • 13. References

    Introduction to RNA-Seq Data Analysis

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    Page last updated: 12-July-16
    Site last generated: Aug 11, 2016