Conditional Expressions
Earlier in the week, we look at how to assign values to variables. Now, we’re going to start looking at how we can compare them. To do this, we use …
Course: Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Passing Command Line Arguments to Bash Scripts
A command line argument is a parameter that we can supply to our Bash script at execution. They allow a user to dynamically affect the actions your script will perform …
Command Line Basics
In this video, Martin is presenting basic Linux commands pwd, cd, ls, rm, mv, mkdir, man. You are welcome to type along, but please beware that you can permanently delete …
Interview with Andy Kirk Part 2 – Visualisation: Art to Empower Data
This is the second part of the interview with Andy Kirk, data visualisation consultant, training provider, teacher, author, speaker, researcher and editor of the award-winning website called visualisingdata.com Watch Fatma …
Bash Arrays
In the previous step we introduced you to Bash variables which can be used to hold temporary information. A variable holds a single value under a single name. By contrast, …
Variables and Their Scope
Bash variables provide temporary storage for information. You can use them to store words/phrases (strings), decimals or integers. Variables To assign a variable, we use the = symbol: name="Victoria" …
Adding Comments to Bash Scripts
Comments are one of the most important things to consider when you are writing your scripts. Making sure that you add comments throughout your scripts is just one of many …
Data Visualisation in R/RStudio – Conclusion and Resources
Data visualisation in R and RStudio makes it possible to easily use basic plotting functions, or apply more advanced functions through packages. As you must have noticed throughout this week, …
Substitutions Using sed
Replacing one text string with another is something we often need to do. This could be because we’ve discovered a repeated typo or misspelling in a file or because we’ve …
Querying and Manipulating Data from Files Using Dedicated Packages in R
Querying and manipulating data from existing files Introduction Querying and manipulating data from files might require you to use advanced options. In R, packages have been developed for specific purposes …
Programming: How to Read Data From Files in R
Introduction Indeed, you will often be willing to exploit the usefulness of built-in functions in R to manipulate large data sets. Although these data sets are organized as data frames, …
How to Create and Manipulate Lists and Data frames in R
Lists and Data frames in R A List is an “object” in R that consist of a collection of other objects known as components. Lists can have components of the …
How to Create and Manipulate Variables and Vectors in R
When working under your current R session, the entities that R creates and uses are called “objects”. There is a wide range of objects that can be created and that …
What is R in computing?
R is a “language and environment for statistical computing and graphics”. R is an integrated suite of facilities for data manipulation, calculation and graphical display. Among other things it has: …
User Input
Watch Victoria presenting simple scripts demonstrating how to capture user input into a script Here are the scripts used in this video: whoami.sh #!/usr/bin/env bashecho "Please enter your name."read nameecho …
These articles are from the online course:
Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R