HPC Software Carpentry - Lesson 4 - Scripts and submitting jobs
Learning Objectives In this lesson you will learn: How to run R on the HPC in 3 different ways (i.e., interactively, via scripts and by submitting jobs)...
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R
geofacets and tidyverse for geographic visualization
Kevin showed us how to use geofacets and other tools within tidyverse to plot COVID-19 and vaccination data organized by geographic entities.
git and github
Wytamma (@wytamma) presented a talk on using git and Github with RStudio. RStudio has great support for git and easily integrated with Github. Github is basi...
Data frame manipulation with tidyr
Here is our introduction to data frame manipulation using tidyr, one of the many useful packages from the tidyverse! Data manipulation is often required whe...
tidyr vs reshape2
An alternative worklfow to Data frame Manipulation with tidyr Created by César Herrera tidyr use can be consulted here Here, I present an alternative way t...
an introduction to Jupyter Notebooks and Jupyter Lab
César (@CexyNature) made an introduction to Jupyter Notebooks and Jupyter Lab, and he showed us how we can use R in Jupyter as an alternative development env...
How to use a profiler to optimise code
Ira (@iracooke) took us through some best practices for writing R code and how to use a profiler to optimise code. Ira’s notes can be found in this repo. li...
Shiny apps in R
Kevin Bairos-Novak (@ecolology) gave an intro to build Shiny apps in R. Kevin’s note can be found in this repo.
How to plot phylogenetic trees in R
Pete (@pete_cowman) gave an intro and demonstrated how to plot phylogenetic trees in R with the package ggtree. After intro he had fun plotting a phylogeny o...
Linear Mixed Effects Models pt2
Ira (@iracooke) summarised the key ideas on random vs fixed effects from the previous meeting, and Sonja walked us through her modelling and model selection ...
Linear Mixed Effects Models
Chloë (@CGBoote) lead us through a tutorial on linear mixed models in R. Lorenzo (@ItsFrogday) has summarised the discussion that followed. Random effects v...
Loops
Anything Goes: Loops Examples from our ‘anything goes’ loop session on 24th of Feb 2020 Python Wytamma presented an algorithm that uses a for loop to calcul...
Using tidyverse to manipulate your data
Pete (@PeteCowman) presented a talk on using tidyverse to manipulate your data. To view Pete’s materials on tidyverse see here.
Intro to RMarkdown
Ira (@iracooke) presented an intro to RMarkdown. The rendered presentation can be viewed on RPubs and source code is on github at https://github.com/iracook...
César
tidyr vs reshape2
An alternative worklfow to Data frame Manipulation with tidyr Created by César Herrera tidyr use can be consulted here Here, I present an alternative way t...
Data Management
César (@CexyNature) did a presentation on Data Management. He described the importance of practicing good data management and he provided advice in what stra...
an introduction to Jupyter Notebooks and Jupyter Lab
César (@CexyNature) made an introduction to Jupyter Notebooks and Jupyter Lab, and he showed us how we can use R in Jupyter as an alternative development env...
Zooming back in
After the Covid-19 disruption which sent us home, we resumed our weekly meetings using Zoom video conference. In this session, César (@CexyNature) showed us ...
Loops
Anything Goes: Loops Examples from our ‘anything goes’ loop session on 24th of Feb 2020 Python Wytamma presented an algorithm that uses a for loop to calcul...
How to use Github
César (@CexyNature) presented a talk on how to use Github. Chloë (@BooteCG), as a way to use his instruction tried to make an .md with the notes/instruction...
Python
an introduction to Jupyter Notebooks and Jupyter Lab
César (@CexyNature) made an introduction to Jupyter Notebooks and Jupyter Lab, and he showed us how we can use R in Jupyter as an alternative development env...
Clean code best practices
Lindsay (@lindsaymarkward) presented a talk via Zoom on clean code best practices with examples in Python. You can find a recoding of the talk on our TouTube...
Zooming back in
After the Covid-19 disruption which sent us home, we resumed our weekly meetings using Zoom video conference. In this session, César (@CexyNature) showed us ...
Python basics 🐍
Wytamma (@wytamma) presented a talk on Python basics 🐍. We used Google colab to write and run some Python.
HPC
HPC Software Carpentry - Lesson 4 - Scripts and submitting jobs
Learning Objectives In this lesson you will learn: How to run R on the HPC in 3 different ways (i.e., interactively, via scripts and by submitting jobs)...
HPC Software Carpentry - Lesson 3 - Transferring files
Learning Objectives In this lesson you will learn: How to transfer files with FileZilla (Mac) and WinSCP (Windows) How to setup an ssh key How to tr...
HPC Software Carpentry - Lesson 2 - BASH fundamentals
Learning Objectives In this lesson you will learn: What is a UNIX command How to create, access and navigate directories using bash How to create an...
HPC Software Carpentry - Lesson 1 - Accessing the HPC
Learning Objectives In this lesson you will learn: The overall structure of the JCU HPC How to obtain a JCU HPC account How to access the JCU HPC ...
Lorenzo
HPC Software Carpentry - Lesson 4 - Scripts and submitting jobs
Learning Objectives In this lesson you will learn: How to run R on the HPC in 3 different ways (i.e., interactively, via scripts and by submitting jobs)...
HPC Software Carpentry - Lesson 3 - Transferring files
Learning Objectives In this lesson you will learn: How to transfer files with FileZilla (Mac) and WinSCP (Windows) How to setup an ssh key How to tr...
HPC Software Carpentry - Lesson 2 - BASH fundamentals
Learning Objectives In this lesson you will learn: What is a UNIX command How to create, access and navigate directories using bash How to create an...
HPC Software Carpentry - Lesson 1 - Accessing the HPC
Learning Objectives In this lesson you will learn: The overall structure of the JCU HPC How to obtain a JCU HPC account How to access the JCU HPC ...
Ira
How to use a profiler to optimise code
Ira (@iracooke) took us through some best practices for writing R code and how to use a profiler to optimise code. Ira’s notes can be found in this repo. li...
Linear Mixed Effects Models pt2
Ira (@iracooke) summarised the key ideas on random vs fixed effects from the previous meeting, and Sonja walked us through her modelling and model selection ...
Intro to RMarkdown
Ira (@iracooke) presented an intro to RMarkdown. The rendered presentation can be viewed on RPubs and source code is on github at https://github.com/iracook...
Chloë
Linear Mixed Effects Models
Chloë (@CGBoote) lead us through a tutorial on linear mixed models in R. Lorenzo (@ItsFrogday) has summarised the discussion that followed. Random effects v...
Loops
Anything Goes: Loops Examples from our ‘anything goes’ loop session on 24th of Feb 2020 Python Wytamma presented an algorithm that uses a for loop to calcul...
How to use Github
César (@CexyNature) presented a talk on how to use Github. Chloë (@BooteCG), as a way to use his instruction tried to make an .md with the notes/instruction...
Wytamma
git and github
Wytamma (@wytamma) presented a talk on using git and Github with RStudio. RStudio has great support for git and easily integrated with Github. Github is basi...
Loops
Anything Goes: Loops Examples from our ‘anything goes’ loop session on 24th of Feb 2020 Python Wytamma presented an algorithm that uses a for loop to calcul...
Python basics 🐍
Wytamma (@wytamma) presented a talk on Python basics 🐍. We used Google colab to write and run some Python.
Statistics
Linear Mixed Effects Models pt2
Ira (@iracooke) summarised the key ideas on random vs fixed effects from the previous meeting, and Sonja walked us through her modelling and model selection ...
Linear Mixed Effects Models
Chloë (@CGBoote) lead us through a tutorial on linear mixed models in R. Lorenzo (@ItsFrogday) has summarised the discussion that followed. Random effects v...
Loops
Anything Goes: Loops Examples from our ‘anything goes’ loop session on 24th of Feb 2020 Python Wytamma presented an algorithm that uses a for loop to calcul...
Kevin
geofacets and tidyverse for geographic visualization
Kevin showed us how to use geofacets and other tools within tidyverse to plot COVID-19 and vaccination data organized by geographic entities.
Data frame manipulation with tidyr
Here is our introduction to data frame manipulation using tidyr, one of the many useful packages from the tidyverse! Data manipulation is often required whe...
Shiny apps in R
Kevin Bairos-Novak (@ecolology) gave an intro to build Shiny apps in R. Kevin’s note can be found in this repo.
Bash
HPC Software Carpentry - Lesson 4 - Scripts and submitting jobs
Learning Objectives In this lesson you will learn: How to run R on the HPC in 3 different ways (i.e., interactively, via scripts and by submitting jobs)...
HPC Software Carpentry - Lesson 3 - Transferring files
Learning Objectives In this lesson you will learn: How to transfer files with FileZilla (Mac) and WinSCP (Windows) How to setup an ssh key How to tr...
HPC Software Carpentry - Lesson 2 - BASH fundamentals
Learning Objectives In this lesson you will learn: What is a UNIX command How to create, access and navigate directories using bash How to create an...
git
git and github
Wytamma (@wytamma) presented a talk on using git and Github with RStudio. RStudio has great support for git and easily integrated with Github. Github is basi...
How to use Github
César (@CexyNature) presented a talk on how to use Github. Chloë (@BooteCG), as a way to use his instruction tried to make an .md with the notes/instruction...
Pete
How to plot phylogenetic trees in R
Pete (@pete_cowman) gave an intro and demonstrated how to plot phylogenetic trees in R with the package ggtree. After intro he had fun plotting a phylogeny o...
Using tidyverse to manipulate your data
Pete (@PeteCowman) presented a talk on using tidyverse to manipulate your data. To view Pete’s materials on tidyverse see here.
Data
Data Management
César (@CexyNature) did a presentation on Data Management. He described the importance of practicing good data management and he provided advice in what stra...
Data storage and reproducible analyses
Joseph M. introduced the issues around Data storage and reproducibility. Started a conversation on producing guidelines and templates for reproducible resear...
tidyverse
Using tidyverse to manipulate your data
Pete (@PeteCowman) presented a talk on using tidyverse to manipulate your data. To view Pete’s materials on tidyverse see here.
Legana
Loops
Anything Goes: Loops Examples from our ‘anything goes’ loop session on 24th of Feb 2020 Python Wytamma presented an algorithm that uses a for loop to calcul...
Reproducibility
Data storage and reproducible analyses
Joseph M. introduced the issues around Data storage and reproducibility. Started a conversation on producing guidelines and templates for reproducible resear...
Phylogenetics
How to plot phylogenetic trees in R
Pete (@pete_cowman) gave an intro and demonstrated how to plot phylogenetic trees in R with the package ggtree. After intro he had fun plotting a phylogeny o...
Shiny
Shiny apps in R
Kevin Bairos-Novak (@ecolology) gave an intro to build Shiny apps in R. Kevin’s note can be found in this repo.
Natalia
HPC Software Carpentry - Lesson 3 - Transferring files
Learning Objectives In this lesson you will learn: How to transfer files with FileZilla (Mac) and WinSCP (Windows) How to setup an ssh key How to tr...