Data Analysis Tutorials
  • Search
  • Github Repo
  • Resources
    • CRAN
    • Bioconductor
    • GitHub
    • Jekyll
    • Girke Lab
    • Jekyll Doc Theme
  • Feedback
     
    • Manuals Under Construction!
    • Overview
      • Introduction
      • Class teaching
    • 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. Graphics in R
      • 14. Analysis Routine
      • 15. R Markdown
      • 16. Session Info
      • 17. References
    • Graphics and Data Visualization in R
      • 1. Overview
      • 2. Base Graphics
      • 3. Grid Graphics
      • 4. lattice Graphics
      • 5. ggplot2 Graphics
      • 6. Specialty Graphics
      • 7. Genome Graphics
      • 8. References
    • Cluster Analysis in R
      • 1. Introduction
      • 2. Data Preprocessing
      • 3. Clustering Algorithms
      • 4. Clustering Exercises
      • 5. Version Information
      • 6. References
    • Programming in R
      • 1. Overview
      • 2. Control Structures
      • 3. Loops
      • 4. Functions
      • 5. Useful Utilities
      • 6. Running R Scripts
      • 7. Building R Packages
      • 8. Programming Exercises
      • 9. Homework 5
      • 10. Session Info
      • 11. References
    • NGS Analysis Basics
      • 1. Overview
      • 2. Package Requirements
      • 3. Strings in R Base
      • 4. Sequences in Bioconductor
      • 5. NGS Sequences
      • 6. Range Operations
      • 7. Transcript Ranges
      • 8. Homework 6
      • 9. Session Info
      • 10. References
    • Designing and Running NGS Workflows
      • 1. Introduction
      • 2. Getting Started
      • 3. Workflow overview
      • 4. Workflow templates
      • 5. Version information
      • 6. References
    • RNA-Seq Workflow Template
      • 1. Introduction
      • 2. Sample definitions and environment settings
      • 3. Read preprocessing
      • 4. Alignments
      • 5. Read quantification per annotation range
      • 6. Analysis of differentially expressed genes with edgeR
      • 7. GO term enrichment analysis of DEGs
      • 8. Clustering and heat maps
      • 9. Version Information
      • 10. Funding
      • 11. References
    • ChIP-Seq Workflow Template
      • 1. Introduction
      • 2. Load workflow environment
      • 3. Read preprocessing
      • 4. Alignments
      • 5. Utilities for coverage data
      • 6. Peak calling with MACS2
      • 7. Annotate peaks with genomic context
      • 8. Count reads overlapping peaks
      • 9. Differential binding analysis
      • 10. GO term enrichment analysis
      • 11. Motif analysis
      • 12. Version Information
      • 13. Funding
      • 14. References
    • VAR-Seq Workflow Template
      • 1. Introduction
      • 2. Load workflow environment
      • 3. Read preprocessing
      • 4. Alignments
      • 5. Variant calling
      • 6. Filter variants
      • 7. Annotate filtered variants
      • 8. Combine annotation results among samples
      • 9. Summary statistics of variants
      • 10. Venn diagram of variants
      • 11. Plot variants programmatically
      • 12. Version Information
      • 13. Funding
      • 14. References
    • Internal notes
      • Administration of site

    Search

      ©2016 UC Riverside. All rights reserved.
      Site last generated: Aug 11, 2016

      Company logo