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A Primer for Computational Biology
A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work.
- Author
- Shawn T. O’Neil
- Publisher
- Oregon State University
- Source
- LibreTexts
- License
- CC BY-NC-SA
- Language
- EN
- Category
- Basic Sciences
Contents· 40 sections
- 01: Introduction to Unix Linux
- 1.01: Context
- 1.02: Logging In
- 1.03: The Command Line and Filesystem
- 1.04: Working with Files and Directories
- 1.05: Permissions and Executables
- 1.06: Installing (Bioinformatics) Software
- 1.07: Command Line BLAST
- 1.08: The Standard Streams
- 1.09: Sorting First and Last Lines
- 1.10: Rows and Columns
- 1.11: Patterns (Regular Expressions)
- 1.12: Miscellanea
- 02: Programming in Python
- 2.01: Hello World
- 2.02: Elementary Data Types
- 2.03: Collections and Looping- Lists and for
- 2.04: File Input and Output
- 2.05: Conditional Control Flow
- 2.06: Python Functions
- 2.07: Command Line Interfacing
- 2.08: Dictionaries
- 2.09: Bioinformatics Knick-knacks and Regular Expressions
- 2.10: Variables and Scope
- 2.11: Objects and Classes
- 2.12: Application Programming Interfaces Modules Packages Syntactic Sugar
- 2.13: Algorithms and Data Structures
- 03: Programming in R
- 3.01: An Introduction
- 3.02: Variables and Data
- 3.03: Vectors
- 3.04: R Functions
- 3.05: Lists and Attributes
- 3.06: Data Frames
- 3.07: Character and Categorical Data
- 3.08: Split Apply Combine
- 3.09: Reshaping and Joining Data Frames
- 3.10: Procedural Programming
- 3.11: Objects and Classes in R
- 3.12: Plotting Data and ggplot2