A Primer for Computational Biology
(2nd Edition)
Preface
Acknowledgements
Dedication
Part 1: The UNIX/Linux Command-Line
1 Context
- Command Lines and Operating Systems
- A Brief History
2 Getting Set Up
3 The Command Line and Filesystem
4 Working with Files and Directories
5 Permissions and Executables
6 Installing (Bioinformatics) Software
7 Using (Bioinformatics) Software
8 Command Line BLAST
9 The Standard Streams
- Filtering Lines, Standard Input
- Counting Simple AT Repeats
10 Sorting, First and Last Lines
- First and Last Lines
11 Rows and columns
- Basic Syntax for awk
12 Patterns (Regular Expressions)
13 Miscellanea
14 Version Control with git
Part 2: Programming in Python
15 Hello, World
- Hello, World
- Making the File Executable
16 Elementary Data Types
17 Collections and Looping: Lists and for
- Tuples (Immutable Lists)
- Looping with for
18 File Input and Output
19 Conditional Control Flow
20 Python Functions
- Important Notes about Functions
- GC Content over Sequences in a File
21 Command Line Interfacing
22 Dictionaries
- Counting Gene Ontology Terms
- Extracting All Lines Matching a Set of IDs
23 String Tips and Regular Expressions
24 Variables and Scope
25 Variables and Classes
- Creating New Classes
26 Use Case: Counting SNPs
27 Application Programming Interfaces, Modules, Packages, Syntactic Sugar
28 Algorithms and Data Structures
Part 3: Programming in R
29 An Introduction
30 Variables and Data
- Numerics, Integers, Characters, and Logicals
31 Vectors
32 R Functions
- Variables and Scope
- Getting Help
33 Lists and Attributes
- Named Lists, Lists within Lists
- Attributes, Removing Elements, List Structure
34 Data Frames
- Data Frame Operations
35 Character and Categorical Data
36 Split, Apply, Combine
37 Reshaping and Joining Data Frames
38 Procedural Programming
39 Objects and Classes in R
- Creating Our Own Classes
40 Plotting Data and ggplot2
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A Primer for Computational Biology (2nd Edition)

Dedication

To the amazing instructors I’ve been fortunate enough to learn from, and to the amazing students I’ve been fortunate enough to learn with.