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@@ -315,12 +315,12 @@ <h1>Overview of workshops</h1>
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<section id="core-programme-overview" class="level3">
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<h3 class="anchored" data-anchor-id="core-programme-overview">Core programme overview</h3>
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<p><strong>Beginner</strong><br>
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<a href="#introduction-to-shell">Introduction to Shell</a><br>
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<a href="#introduction-to-the-r-programming-language">Introduction to R</a><br>
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<a href="#introduction-to-shell-for-bioinformatics">Introduction to Shell for bioinformatics</a><br>
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<a href="#introduction-to-r-for-bioinformatics">Introduction to R for bioinformatics</a><br>
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<a href="#rna-seq-data-analysis">RNA-seq Data Analysis</a></p>
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<p><strong>Intermediate</strong><br>
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<a href="#intermediate-shell-for-bioinformatics">Intermediate Shell</a><br>
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<a href="#intermediate-r">Intermediate R</a><br>
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<a href="#intermediate-shell-for-bioinformatics">Intermediate Shell for bioinformatics</a><br>
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<a href="#intermediate-r-for-bioinformatics">Intermediate R for bioinformatics</a><br>
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<a href="#introduction-to-bash-scripting-and-hpc-job-scheduler">Introduction to Bash Scripting and HPC Job Scheduler</a></p>
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<p><strong>Specialised</strong><br>
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<a href="#visualisation-with-ggplot2">Visualisation with ggplot2</a><br>
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<p><em>Our series of introductory workshops are designed to take you from absolute beginner to self-driving learner. Each of these workshops can be done as a standalone crash course in a particular topic, and they can also be strung together to provide a strong foundation in bioinformatics principals and practices.</em></p>
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</section>
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<hr>
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<section id="introduction-to-shell" class="level3 workshop-header workshop-block">
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<h3 class="workshop-header anchored" data-anchor-id="introduction-to-shell">Introduction to Shell</h3>
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<section id="introduction-to-shell-for-bioinformatics" class="level3 workshop-header workshop-block">
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<h3 class="workshop-header anchored" data-anchor-id="introduction-to-shell-for-bioinformatics">Introduction to Shell for bioinformatics</h3>
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<p><img src="assets/workshop-mainpage-image/introtoshell.png" alt="Welcome to Shell" class="workshop-image"></p>
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<p>Learn the fundamentals of working with the Command Line Interface (CLI). Shell is a program that allows you to interact with the command line. Familiarity with the shell will allow you to access remote servers, automate tasks, and use a wide range of tools that are unavailable on a Graphical User Interface (GUI).</p>
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<p>During this workshop you will learn:</p>
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<strong>View the full workshop material here:</strong> <a href="https://genomicsaotearoa.github.io/introduction-to-shell/">Introduction to Shell</a></p>
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</section>
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<hr>
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<section id="introduction-to-the-r-programming-language" class="level3 workshop-header workshop-block">
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<h3 class="workshop-header anchored" data-anchor-id="introduction-to-the-r-programming-language">Introduction to the R Programming Language</h3>
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<section id="introduction-to-r-for-bioinformatics" class="level3 workshop-header workshop-block">
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<h3 class="workshop-header anchored" data-anchor-id="introduction-to-r-for-bioinformatics">Introduction to R for bioinformatics</h3>
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<p><img src="assets/workshop-mainpage-image/Rlogo-colour.jpeg" alt="R logo" class="workshop-image"></p>
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<p>Get started with R, a highly popular programming language in the fields of biology and statistics. R is world-renowned for producing high-quality, publication-ready figures and tables.<br>
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Note that this workshop is a pre-requisite for the RNA-seq Data Analysis workshop and intermediate R workshops.<br>
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<strong>View the full workshop material here:</strong> <a href="https://genomicsaotearoa.github.io/shell-for-bioinformatics/">Intermediate Shell for Bioinformatics</a></p>
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</section>
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<hr>
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<section id="intermediate-r" class="level3 workshop-header workshop-block">
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<h3 class="workshop-header anchored" data-anchor-id="intermediate-r">Intermediate R</h3>
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<section id="intermediate-r-for-bioinformatics" class="level3 workshop-header workshop-block">
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<h3 class="workshop-header anchored" data-anchor-id="intermediate-r-for-bioinformatics">Intermediate R for bioinformatics</h3>
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<p><img src="assets/workshop-mainpage-image/intermed-r-logo.png" alt="Intermediate R logo" class="workshop-image"></p>
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<p>Advance your skills with R! You will learn to complete R tasks with fewer lines of code, scale your analyses, and write readable code.<br>
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Some of the topics covered in the workshop are:</p>

portfolio.qmd

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### Core programme overview
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**Beginner**
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[Introduction to Shell](#introduction-to-shell)
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[Introduction to R](#introduction-to-the-r-programming-language)
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[Introduction to Shell for bioinformatics](#introduction-to-shell-for-bioinformatics)
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[Introduction to R for bioinformatics](#introduction-to-r-for-bioinformatics)
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[RNA-seq Data Analysis](#rna-seq-data-analysis)
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**Intermediate**
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[Intermediate Shell](#intermediate-shell-for-bioinformatics)
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[Intermediate R](#intermediate-r)
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[Intermediate Shell for bioinformatics](#intermediate-shell-for-bioinformatics)
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[Intermediate R for bioinformatics](#intermediate-r-for-bioinformatics)
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[Introduction to Bash Scripting and HPC Job Scheduler](#introduction-to-bash-scripting-and-hpc-job-scheduler)
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::: {.workshop-block}
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### Introduction to Shell {.workshop-header}
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### Introduction to Shell for bioinformatics {.workshop-header}
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<img src="assets/workshop-mainpage-image/introtoshell.png" alt="Welcome to Shell" class="workshop-image">
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::: {.workshop-block}
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### Introduction to the R Programming Language {.workshop-header}
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### Introduction to R for bioinformatics {.workshop-header}
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<img src="assets/workshop-mainpage-image/Rlogo-colour.jpeg" alt="R logo" class="workshop-image">
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---
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::: {.workshop-block}
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### Intermediate R {.workshop-header}
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### Intermediate R for bioinformatics {.workshop-header}
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<img src="assets/workshop-mainpage-image/intermed-r-logo.png" alt="Intermediate R logo" class="workshop-image">
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