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Table of Contents

Table of Contents

 

        Preface

        Acknowledgements

        Dedication

    Part I: Introduction to Unix/Linux

        Context

        Logging In

        The Command Line and Filesystem

        Working with Files and Directories

        Permissions and Executables

        Installing (Bioinformatics) Software

        Command Line BLAST

        The Standard Streams

        Sorting, First and Last Lines

        Rows and Columns

        Patterns (Regular Expressions)

        Miscellanea

 

    Part II: Programming in Python

        Hello, World

        Elementary Data Types

        Collections and Looping: Lists and for

        File Input and Output

        Conditional Control Flow

        Python Functions

        Command Line Interfacing

        Dictionaries

        Bioinformatics Knick-knacks and Regular Expressions

        Variables and Scope

        Objects and Classes

        Application Programming Interfaces, Modules, Packages, Syntactic Sugar

        Algorithms and Data Structures

 

    Part III: Programming in R

        An Introduction

        Variables and Data

        Vectors

        R Functions

        Lists and Attributes

        Data Frames

        Character and Categorical Data

        Split, Apply, Combine

        Reshaping and Joining Data Frames

        Procedural Programming

        Objects and Classes in R

        Plotting Data and ggplot2

 

        Files

        Index

        About the Author

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