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Preface
Acknowledgements
Dedication
1. Context
2. Logging In
3. The Command Line and Filesystem
4. Working with Files and Directories
5. Permissions and Executables
6. Installing (Bioinformatics) Software
7. Command Line BLAST
8. The Standard Streams
9. Sorting, First and Last Lines
10. Rows and Columns
11. Patterns (Regular Expressions)
12. Miscellanea
13. Hello, World
14. Elementary Data Types
15. Collections and Looping: Lists and for
16. File Input and Output
17. Conditional Control Flow
18. Python Functions
19. Command Line Interfacing
20. Dictionaries
21. Bioinformatics Knick-knacks and Regular Expressions
22. Variables and Scope
23. Objects and Classes
24. Application Programming Interfaces, Modules, Packages, Syntactic Sugar
25. Algorithms and Data Structures
26. An Introduction
27. Variables and Data
28. Vectors
29. R Functions
30. Lists and Attributes
31. Data Frames
32. Character and Categorical Data
33. Split, Apply, Combine
34. Reshaping and Joining Data Frames
35. Procedural Programming
36. Objects and Classes in R
37. Plotting Data and ggplot2
Files
Index
About the Author
Creative Commons License
Recommended Citations
Versioning
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A Primer for Computational Biology Copyright © 2019 by Shawn T. O'Neil is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.