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R programming

  1. Introduction
  2. R Basics
  3. Code Editors for R
  4. Integrating R with Vim and Tmux
  5. Finding Help
  6. Control Structures
    1. 6.1 Conditional Executions
      1. 6.1.1 Comparison Operators
      2. 6.1.2 Logical Operators
      3. 6.1.3 If Statements
      4. 6.1.4 Ifelse Statements
    2. 6.2 Loops
      1. 6.2.1 For Loop
      2. 6.2.2 While Loop
      3. 6.2.3 Apply Loop Family
        1. 6.2.3.1 For Two-Dimensional Data Sets: apply
        2. 6.2.3.2 For Ragged Arrays: tapply
        3. 6.2.3.3 For Vectors and Lists: lapply and sapply
      4. 6.2.4 Other Loops
      5. 6.2.5 Improving Speed Performance of Loops
  7. Functions
  8. Useful Utilities
    1. 8.1 Debugging Utilities
    2. 8.2 Regular Expressions
    3. 8.3 Interpreting Character String as Expression
    4. 8.4 Time, Date and Sleep
    5. 8.5 Calling External Software with System Command
    6. 8.6 Miscellaneous Utilities
  9. Running R Programs
  10. 10 Object-Oriented Programming (OOP)
    1. 10.1 Define S4 Classes
    2. 10.2 Assign Generics and Methods
  11. 11 Building R Packages
  12. 12 Reproducible Research by Integrating R with Latex or Markdown
  13. 13 R Programming Exercises
    1. 13.1 Exercise Slides
    2. 13.2 Sample Scripts
      1. 13.2.1 Batch Operations on Many Files
      2. 13.2.2 Large-scale Array Analysis
      3. 13.2.3 Graphical Procedures: Feature Map Example
      4. 13.2.4 Sequence Analysis Utilities
      5. 13.2.5 Pattern Matching and Positional Parsing of Sequences
      6. 13.2.6 Identify Over-Represented Strings in Sequence Sets
      7. 13.2.7 Translate DNA into Protein
      8. 13.2.8 Subsetting of Structure Definition Files (SDF)
      9. 13.2.9 Managing Latex BibTeX Databases
      10. 13.2.10 Loan Payments and Amortization Tables
      11. 13.2.11 Course Assignment: GC Content, Reverse & Complement

Course Curriculum

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