1. Home
  2. Materials
Register training material
41 materials found

Authors: Harrison, Paul (orcid: 0000...  or Intersect Australia 

Randomised Controlled Trials with REDCap

REDCap is a powerful and extensible application for managing and running longitudinal data collection activities. In this course, learn how to manage a Randomised Controlled Trial using REDCap, including the randomisation module, adverse event reporting and automated participant withdrawals. This...

Keywords: REDCap

Randomised Controlled Trials with REDCap https://dresa.org.au/materials/randomised-controlled-trials-with-redcap REDCap is a powerful and extensible application for managing and running longitudinal data collection activities. In this course, learn how to manage a Randomised Controlled Trial using REDCap, including the randomisation module, adverse event reporting and automated participant withdrawals. This course will introduce some of REDCap’s more advanced features for running randomised trials, and builds on the material taught in REDCAP201 – Longitudinal Trials with REDCap. - Create Data Access Groups (DAGs) and assign users to manage trial sites - Build randomisation allocation table  - Enable and implement participant randomisation module - Design an adverse reporting system using Automated Survey Invitations and Alerts - Create an automated participant withdrawal process - Customise record dashboards Learners should have a solid understanding of REDCap and be familiar with the content of [Data Capture and Surveys with REDCap](https://intersectaustralia.github.io/training/REDCAP101/) and [Longitudinal Trials with REDCap](https://intersectaustralia.github.io/training/REDCAP201/). training@intersect.org.au REDCap
Data Entry, Exploration, & Analysis in SPSS

This hands-on training is designed to familiarize you with the interface and basic data processing functionalities in SPSS. We will examine several “must know” syntax commands that can help streamline data entry and processing. In addition, we will explore how to obtain descriptive statistics in...

Keywords: SPSS

Data Entry, Exploration, & Analysis in SPSS https://dresa.org.au/materials/data-entry-exploration-analysis-in-spss This hands-on training is designed to familiarize you with the interface and basic data processing functionalities in SPSS. We will examine several “must know” syntax commands that can help streamline data entry and processing. In addition, we will explore how to obtain descriptive statistics in SPSS and perform visualization. This workshop is recommended for researchers and postgraduate students who are new to SPSS or Statistics; or those simply looking for a refresher course before taking a deep dive into using SPSS, either to apply it to their research or to add it to their arsenal of eResearch skills. - Navigate SPSS Variable and Data views. - Create and describe data from scratch. - Import Data from Excel. - Familiarise yourself with exploratory data analysis (EDA), including: - Understand variable types, identity missing data and outliers. - Visualise data in graphs and tables. - Compose SPSS Syntax to repeat and store analysis steps. - Generate a report testing assumptions of statistical tests. - Additional exercises: - Check assumptions for common statistical tests. - Make stunning plots. In order to participate, attendees must have a licensed copy of SPSS installed on their computer. Speak to your local university IT or Research Office for assistance in obtaining a license and installing the software. training@intersect.org.au SPSS
WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires...

Keywords: bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-6a1126cf-7105-43ec-bf55-7c492f758301 This record includes training materials associated with the Australian BioCommons workshop 'Single cell RNAseq analysis in R'. This workshop took place over two, 3.5 hour sessions on 26 and 27 October 2023.Event descriptionAnalysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data. We will discuss the 'why' behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data.This workshop is presented by the Australian BioCommons, Queensland Cyber Infrastructure Foundation (QCIF) and the Monash Genomics and Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.Lead trainers: Sarah Williams, Adele Barugahare, Paul Harrison, Laura Perlaza JimenezFacilitators: Nick Matigan, Valentine Murigneux, Magdalena (Magda) AntczakInfrastructure provision: Uwe WinterCoordinator: Melissa BurkeTraining materialsMaterials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.Files and materials included in this record:Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshopMaterials shared elsewhere:This workshop follows the tutorial 'scRNAseq Analysis in R with Seurat'https://swbioinf.github.io/scRNAseqInR_Doco/index.htmlSlides used to introduce key topics are available via GitHubhttps://github.com/swbioinf/scRNAseqInR_Doco/tree/main/slidesThis material is based on the introductory Guided Clustering Tutorial tutorial from Seurat.It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here.   Melissa Burke (melissa@biocommons.org.au) bioinformatics, transcriptomics, single cell RNA-seq, Seurat, R statistical software
WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.

Event description

Analysis and interpretation of single cell RNAseq (scRNAseq) data...

Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/workshop-single-cell-rnaseq-analysis-in-r-4f60b82d-2f1e-4021-9569-6955878dd945 This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022. Event description Analysis and interpretation of single cell RNAseq (scRNAseq) data requires dedicated workflows. In this hands-on workshop we will show you how to perform single cell analysis using Seurat - an R package for QC, analysis, and exploration of single-cell RNAseq data.  We will discuss the ‘why’ behind each step and cover reading in the count data, quality control, filtering, normalisation, clustering, UMAP layout and identification of cluster markers. We will also explore various ways of visualising single cell expression data. This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.   Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. scRNAseq_Slides (PDF): Slides used to introduce topics scRNAseq_Schedule (PDF): A breakdown of the topics and timings for the workshop scRNAseq_Resources (PDF): A list of resources recommended by trainers and participants scRNAseq_QandA(PDF): Archive of questions and their answers from the workshop Slack Channel.   Materials shared elsewhere: This workshop follows the tutorial ‘scRNAseq Analysis in R with Seurat’ https://swbioinf.github.io/scRNAseqInR_Doco/index.html This material is based on the introductory Guided Clustering Tutorial tutorial from Seurat. It is also drawing from a similar workshop held by Monash Bioinformatics Platform Single-Cell-Workshop, with material here. Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq
WORKSHOP: Working with genomics sequences and features in R with Bioconductor

This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021.

Workshop description

Explore the many useful functions that the Bioconductor...

Keywords: R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis

WORKSHOP: Working with genomics sequences and features in R with Bioconductor https://dresa.org.au/materials/workshop-working-with-genomics-sequences-and-features-in-r-with-bioconductor-8399bf0d-1e9e-48f3-a840-3f70f23254bb This record includes training materials associated with the Australian BioCommons workshop ‘Working with genomics sequences and features in R with Bioconductor’. This workshop took place on 23 September 2021. Workshop description Explore the many useful functions that the Bioconductor environment offers for working with genomic data and other biological sequences.  DNA and proteins are often represented as files containing strings of nucleic acids or amino acids. They are associated with text files that provide additional contextual information such as genome annotations. This workshop provides hands-on experience with tools, software and packages available in R via Bioconductor for manipulating, exploring and extracting information from biological sequences and annotation files. We will look at tools for working with some commonly used file formats including FASTA, GFF3, GTF, methods for identifying regions of interest, and easy methods for obtaining data packages such as genome assemblies.  This workshop is presented by the Australian BioCommons and Monash Bioinformatics Platform with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative. Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop providing a breakdown of topics and timings   Materials shared elsewhere: This workshop follows the tutorial ‘Working with DNA sequences and features in R with Bioconductor - version 2’ developed for Monash Bioinformatics Platform and Monash Data Fluency by Paul Harrison. https://monashdatafluency.github.io/r-bioc-2/ Melissa Burke (melissa@biocommons.org.au) R software, Bioconductor, Bioinformatics, Analysis, Genomics, Sequence analysis
Beyond Basics: Conditionals and Visualisation in Excel

After cleaning your dataset, you may need to apply some conditional analysis to glean greater insights from your data. You may also want to enhance your charts for inclusion into a manuscript, thesis or report by adding some statistical elements. This course will cover conditional syntax, nested...

Keywords: Excel

Beyond Basics: Conditionals and Visualisation in Excel https://dresa.org.au/materials/beyond-basics-conditionals-and-visualisation-in-excel After cleaning your dataset, you may need to apply some conditional analysis to glean greater insights from your data. You may also want to enhance your charts for inclusion into a manuscript, thesis or report by adding some statistical elements. This course will cover conditional syntax, nested functions, statistical charting and outlier identification. Armed with the tips and tricks from our introductory Excel for Researchers course, you will be able to tap into even more of Excel’s diverse functionality and apply it to your research project. - Cell syntax and conditional formatting - IF functions - Pivot Table summaries - Nesting multiple AND/IF/OR calculations - Combining nested calculations with conditional formatting to bring out important elements of the dataset - MINIFS function - Box plot creation and outlier identification - Trendline and error bar chart enhancements Familiarity with the content of Excel for Researchers, specifically:  - the general Office/Excel interface (menus, ribbons/toolbars, etc.) - workbooks and worksheets - absolute and relative references, e.g. $A$1, A1. - simple ranges, e.g. A1:B5 training@intersect.org.au Excel
Data Capture and Surveys with REDCap

Would you like to enable secure and reliable data collection forms and manage online surveys? Would your study benefit from web-based data entry? Research Electronic Data Capture (REDCap) might be for you.

This course will introduce you to REDCap, a rapidly evolving web tool developed by...

Keywords: REDCap

Data Capture and Surveys with REDCap https://dresa.org.au/materials/data-capture-and-surveys-with-redcap Would you like to enable secure and reliable data collection forms and manage online surveys? Would your study benefit from web-based data entry? Research Electronic Data Capture (REDCap) might be for you. This course will introduce you to REDCap, a rapidly evolving web tool developed by researchers for researchers. REDCap features a high level of security, and a high degree of customisability for your forms and advanced user access control. It also features free, unlimited survey distribution functionality and a sophisticated export module with support for all standard statistical programs. Get started with REDCap Create and set up projects Design forms and surveys using the online designer Learn how to use branching logic, piping, and calculations Enter data via forms and distribute surveys Create, view and export data reports Add collaborators and set their privileges The course has no prerequisites. training@intersect.org.au REDCap
Research Data Management Techniques

Are you drowning in research data? Do you want to know where you should be storing your data? Are you required to comply with funding body data management requirements, but don’t know how?

This workshop is ideal for researchers who want to know how research data management can support...

Keywords: Data Management

Research Data Management Techniques https://dresa.org.au/materials/research-data-management-techniques Are you drowning in research data? Do you want to know where you should be storing your data? Are you required to comply with funding body data management requirements, but don’t know how? This workshop is ideal for researchers who want to know how research data management can support project success and are interested in research data management services and support available at their institution. Combining slide-based background material, discussions, and case studies this workshop will equip participants with best practices for managing their valuable research data. How to manage research data according to legal, statutory, ethical, funding body and university requirements Approaches to planning, collecting, organising, managing, storing, backing up, preserving, and sharing your data Services supporting research data at your institution The course has no prerequisites. training@intersect.org.au Data Management
Introduction to Machine Learning using R: SVM & Unsupervised Learning

Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore...

Keywords: R

Introduction to Machine Learning using R: SVM & Unsupervised Learning https://dresa.org.au/materials/introduction-to-machine-learning-using-r-svm-unsupervised-learning Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the R programming language and its scientific computing packages. Comprehensive introduction to Machine Learning models and techniques such as Support Vector Machine, K-Nearest Neighbor and Dimensionality Reduction. Know the differences between various core Machine Learning models. Understand the Machine Learning modelling workflows. Use R and its relevant packages to process real datasets, train and apply Machine Learning models. \\Either \Learn to Program: R\ and \Data Manipulation in R\ or \Learn to Program: R\ and \Data Manipulation and Visualisation in R\needed to attend this course. If you already have experience with programming, please check the topics covered in the courses above and \Introduction to ML using R: Introduction & Linear Regression\ to ensure that you are familiar with the knowledge needed for this course, such as good understanding of R syntax and basic programming concepts, familiarity with dplyr, tidyr and ggplot2 packages, and basic understanding of Machine Learning and Model Training.\\Maths knowledge is not required. There are only a few Math formula that you are going to see in this course, however references to Mathematics required for learning about Machine Learning will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them.\\ training@intersect.org.au R
Longitudinal Trials with REDCap

REDCap is a powerful and extensible application for managing and running longitudinal data collection activities. With powerful features such as organising data collection instruments into predefined events, you can shepherd your participants through a complex survey at various time points with...

Keywords: REDCap

Longitudinal Trials with REDCap https://dresa.org.au/materials/longitudinal-trials-with-redcap REDCap is a powerful and extensible application for managing and running longitudinal data collection activities. With powerful features such as organising data collection instruments into predefined events, you can shepherd your participants through a complex survey at various time points with very little configuration. This course will introduce some of REDCap’s more advanced features for running longitudinal studies, and builds on the foundational material taught in REDCAP101 – Managing Data Capture and Surveys with REDCap. Build a longitudinal project Manage participants throughout multiple events Configure and use Automated Survey Invitations Use Smart Variables to add powerful features to your logic Take advantage of high-granularity permissions for your collaborators Understand the data structure of a longitudinal project This course requires the participant to have a fairly good basic knowledge of REDCap. To come up to speed, consider taking our \Data Capture and Surveys with REDCap\ workshop. training@intersect.org.au REDCap
Introduction to Machine Learning using R: Introduction & Linear Regression

Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore...

Keywords: R

Introduction to Machine Learning using R: Introduction & Linear Regression https://dresa.org.au/materials/introduction-to-machine-learning-using-r-introduction-linear-regression Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the R programming language and its scientific computing packages. Understand the difference between supervised and unsupervised Machine Learning. Understand the fundamentals of Machine Learning. Comprehensive introduction to Machine Learning models and techniques such as Linear Regression and Model Training. Understand the Machine Learning modelling workflows. Use R and and its relevant packages to process real datasets, train and apply Machine Learning models \\Either \Learn to Program: R\ and \Data Manipulation in R\ or \Learn to Program: R\ and \Data Manipulation and Visualisation in R\needed to attend this course. If you already have experience with programming, please check the topics covered in courses above to ensure that you are familiar with the knowledge needed for this course, such as good understanding of R syntax and basic programming concepts and familiarity with dplyr, tidyr and ggplot2 packages.\\Maths knowledge is not required. There are only a few Math formula that you are going to see in this course, however references to Mathematics required for learning about Machine Learning will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them.\\ training@intersect.org.au R
Exploring ANOVAs in R

R is quickly gaining popularity as a programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework.This half-day course covers one and two-way Analyses of Variance (ANOVA) and their...

Keywords: R

Exploring ANOVAs in R https://dresa.org.au/materials/exploring-anovas-in-r R is quickly gaining popularity as a programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework.This half-day course covers one and two-way Analyses of Variance (ANOVA) and their non-parametric counterparts in R. ANOVA (Analysis of Variance) is a statistical method used to determine whether there are significant differences between the means of three or more groups. It helps analyse the effect of independent variables on a dependent variable by comparing the variance within groups to the variance between groups. ANOVA tests assume normality, homogeneity of variances, and independence of observations, and can be used to explore relationships in datasets, such as how factors like study time or parental education affect student performance. - Basic statistical theory behind ANOVAs - How to check that the data meets the assumptions - One-way ANOVA in R and post-hoc analysis - Two-way ANOVA plus interaction effects and post-hoc analysis - Non-parametric alternatives to one and two-way ANOVA This course assumes an intermediate level of programming proficiency, plus familiarity with the syntax and functions of the dplyr and ggplot2 packages. Experience navigating the RStudio integrated development environment (IDE) is also required. If you’re new to programming in R, we strongly recommend you register for the \Learn to Program: R\, \Data Manipulation and Visualisation in R\ workshops first.  training@intersect.org.au R
Cleaning Data with Open Refine

Do you have messy data from multiple inconsistent sources, or open-responses to questionnaires? Do you want to improve the quality of your data by refining it and using the power of the internet?

Open Refine is the perfect partner to Excel. It is a powerful, free tool for exploring,...

Keywords: Open Refine

Cleaning Data with Open Refine https://dresa.org.au/materials/cleaning-data-with-open-refine Do you have messy data from multiple inconsistent sources, or open-responses to questionnaires? Do you want to improve the quality of your data by refining it and using the power of the internet? Open Refine is the perfect partner to Excel. It is a powerful, free tool for exploring, normalising and cleaning datasets, and extending data by accessing the internet through APIs. In this course we’ll work through the various features of Refine, including importing data, faceting, clustering, and calling remote APIs, by working on a fictional but plausible humanities research project. Download, install and run Open Refine Import data from csv, text or online sources and create projects Navigate data using the Open Refine interface Explore data by using facets Clean data using clustering Parse data using GREL syntax Extend data using Application Programming Interfaces (APIs) Export project for use in other applications The course has no prerequisites. training@intersect.org.au Open Refine
Collecting Web Data

Web scraping is a technique for extracting information from websites. This can be done manually but it is usually faster, more efficient and less error-prone if it can be automated.

Web scraping allows you to convert non-tabular or poorly structured data into a usable, structured format,...

Keywords: Python

Collecting Web Data https://dresa.org.au/materials/collecting-web-data Web scraping is a technique for extracting information from websites. This can be done manually but it is usually faster, more efficient and less error-prone if it can be automated. Web scraping allows you to convert non-tabular or poorly structured data into a usable, structured format, such as a .csv file or spreadsheet. But scraping is about more than just acquiring data: it can help you track changes to data online, and help you archive data. In short, it’s a skill worth learning. So join us for this web scraping workshop to learn web scraping, using the researcher-focused training modules from the highly regarded Software Carpentry Foundation. The concept of structured data The use of XPath queries on HTML document How to scrape data using browser extensions How to scrape using Python and Scrapy How to automate the scraping of multiple web pages A good knowledge of the basic concepts and techniques in Python. Consider taking our \Learn to Program: Python\ and \Python for Research\ courses to come up to speed beforehand. training@intersect.org.au Python
Mastering text with Regular Expressions

Have you ever wanted to extract phone numbers out of a block of unstructured text? Or email addresses. Or find all the words that start with “e” and end with “ed”, no matter their length? Or search through DNA sequences for a pattern? Or extract coordinates from GPS data?

Regular...

Keywords: Regular Expressions

Mastering text with Regular Expressions https://dresa.org.au/materials/mastering-text-with-regular-expressions Have you ever wanted to extract phone numbers out of a block of unstructured text? Or email addresses. Or find all the words that start with “e” and end with “ed”, no matter their length? Or search through DNA sequences for a pattern? Or extract coordinates from GPS data? Regular Expressions (regexes) are a powerful way to handle a multitude of different types of data. They can be used to find patterns in text and make sophisticated replacements. Think of them as find and replace on steroids. Come along to this workshop to learn what they can do and how to apply them to your research. Comprehend and apply the syntax of regular expressions Use the http://regexr.com tool to test a regular expression against some text Construct simple regular expressions to find capitalised words; all numbers; all words that start with a specific set of letters, etc. in a block of text Craft and test a progressively more complex regular expression Find helpful resources covering regular expressions on the web Comprehend and apply the syntax of regular expressions Use the http://regexr.com tool to test a regular expression against some text Construct simple regular expressions to find capitalised words; all numbers; all words that start with a specific set of letters, etc. in a block of text Craft and test a progressively more complex regular expression Find helpful resources covering regular expressions on the web training@intersect.org.au Regular Expressions
Data Manipulation and Visualisation in R

R is quickly gaining popularity as a programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework.

In this workshop, you will learn how to manipulate, explore and get insights...

Keywords: R

Data Manipulation and Visualisation in R https://dresa.org.au/materials/data-manipulation-and-visualisation-in-r R is quickly gaining popularity as a programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework. In this workshop, you will learn how to manipulate, explore and get insights from your data (Data Manipulation using the dplyr package), as well as how to convert your data from one format to another (Data Transformation using the tidyr package). You will also explore different types of graphs and learn how to customise them using one of the most popular plotting packages in R, ggplot2 (Data Visualisation). We teach using RStudio, which allows program code, results, visualisations and documentation to be blended seamlessly. Join us for a live coding workshop where we write programs that produce results, using the researcher-focused training modules from Intersect and the highly regarded Software Carpentry Foundation. DataFrame Manipulation using the dplyr package DataFrame Transformation using the tidyr package Using the Grammar of Graphics to convert data into figures using the ggplot2 package Configuring plot elements within ggplot2 Exploring different types of plots using ggplot2 Either \Learn to Program: R\ or \Learn to Program: R\ and \R for Research\ needed to attend this course. If you already have experience with programming, please check the topics covered in the \Learn to Program: R\ and \R for Research\ courses to ensure that you are familiar with the knowledge needed for this course. training@intersect.org.au R
Traversing t tests in R

R has become a popular programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework.

The primary goal of this workshop is to familiarise you with basic statistical concepts in R...

Keywords: R

Traversing t tests in R https://dresa.org.au/materials/traversing-t-tests-in-r R has become a popular programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework. The primary goal of this workshop is to familiarise you with basic statistical concepts in R from reading in and manipulating data, checking assumptions, statistical tests and visualisations. This is not an advanced statistics course, but is instead designed to gently introduce you to statistical comparisons and hypothesis testing in R. Read in and manipulate data Check assumptions of t tests Perform one-sample t tests Perform two-sample t tests (Independent-samples, Paired-samples) Perform nonparametric t tests (One-sample Wilcoxon Signed Rank test, Independent-samples Mann-Whitney U test) This course assumes familiarity with R and RStudio. You should have a good understanding of R syntax and basic programming concepts. Please consider attending Intersect’s following courses to get up to speed: \Learn to Program: R\, \Data Manipulation and Visualisation in R\ training@intersect.org.au R
Introduction to Machine Learning using R: Classification

Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore...

Keywords: R

Introduction to Machine Learning using R: Classification https://dresa.org.au/materials/introduction-to-machine-learning-using-r-classification Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the R programming language and its scientific computing packages. Comprehensive introduction to Machine Learning models and techniques such as Logistic Regression, Decision Trees and Ensemble Learning. Know the differences between various core Machine Learning models. Understand the Machine Learning modelling workflows. Use R and its relevant packages to process real datasets, train and apply Machine Learning models. \\Either \Learn to Program: R\ and \Data Manipulation in R\ or \Learn to Program: R\ and \Data Manipulation and Visualisation in R\needed to attend this course. If you already have experience with programming, please check the topics covered in courses above and \Introduction to ML using R: Introduction & Linear Regression\ to ensure that you are familiar with the knowledge needed for this course, such as good understanding of R syntax and basic programming concepts, familiarity with dplyr, tidyr and ggplot2 packages, and basic understanding of Machine Learning and Model Training.\\Maths knowledge is not required. There are only a few Math formula that you are going to see in this course, however references to Mathematics required for learning about Machine Learning will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them.\\ training@intersect.org.au R
Data Visualisation in R

R is quickly gaining popularity as a programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework.

In this workshop, you will explore different types of graphs and learn how to...

Keywords: R

Data Visualisation in R https://dresa.org.au/materials/data-visualisation-in-r R is quickly gaining popularity as a programming language for statisticians, data scientists and researchers. It has an excellent ecosystem including the powerful RStudio and the Shiny web application framework. In this workshop, you will explore different types of graphs and learn how to customise them using one of the most popular plotting packages in R, ggplot2 (Data Visualisation). We teach using RStudio, which allows program code, results, visualisations and documentation to be blended seamlessly. Join us for a live coding workshop where we write programs that produce results, using the researcher-focused training modules from Intersect and the highly regarded Software Carpentry Foundation. Using the Grammar of Graphics to convert data into figures using the ggplot2 package Configuring plot elements within ggplot2 Exploring different types of plots using ggplot2 Either \Learn to Program: R\ or \Learn to Program: R\ and \R for Research\ needed to attend this course. If you already have experience with programming, please check the topics covered in the \Learn to Program: R\ and \R for Research\ courses to ensure that you are familiar with the knowledge needed for this course. We also strongly recommend attending the \Data Manipulation in R\ course. training@intersect.org.au R
Exploring Chi-square and correlation in R

This hands-on training is designed to familiarise you with the data analysis environment of the R programming. In this session, we will traverse into the realm of inferential statistics, beginning with correlation and reliability. We will present a brief conceptual overview and the R procedures...

Keywords: R

Exploring Chi-square and correlation in R https://dresa.org.au/materials/exploring-chi-square-and-correlation-in-r This hands-on training is designed to familiarise you with the data analysis environment of the R programming. In this session, we will traverse into the realm of inferential statistics, beginning with correlation and reliability. We will present a brief conceptual overview and the R procedures for computing reliability and correlation (Pearson’s r, Spearman’s Rho and Kendall’s tau) in real world datasets. Obtain inferential statistics and assess data normality Manipulate data and create graphs Perform Chi-Square tests (Goodness of Fit test and Test of Independence) Perform correlations on continuous and categorical data (Pearson’s r, Spearman’s Rho and Kendall’s tau) This course assumes familiarity with R and RStudio. You should have a good understanding of R syntax and basic programming concepts, as well as familiarity with data manipulation (dplyr) and visualisation (ggplot2 package).  Please consider attending Intersect’s following courses to get up to speed: \Learn to Program: R\, \Data Manipulation and Visualisation in R\ training@intersect.org.au R
Regular Expressions on the Command Line

Would you like to use regular expressions with the classic command line utilities find, grep, sed and awk? These venerable Unix utilities allow you to search, filter and transform large amounts of text (including many common data formats) efficiently and repeatably.

find to locate files and...

Keywords: Regular Expressions

Regular Expressions on the Command Line https://dresa.org.au/materials/regular-expressions-on-the-command-line Would you like to use regular expressions with the classic command line utilities find, grep, sed and awk? These venerable Unix utilities allow you to search, filter and transform large amounts of text (including many common data formats) efficiently and repeatably. find to locate files and directories matching regexes. grep to filter lines in files based on pattern matches. sed to find and replace using regular expressions and captures. awk to work with row- and column-oriented data. This course assumes prior knowledge of the basic syntax of regular expressions. If you’re new to regular expressions or would like a refresher, take our Mastering text with Regular Expressions course first. This course also assumes basic familiarity with the Bash command line environment found on GNU/Linux and other Unix-like environments. Take our Unix Shell and Command Line Basics course to get up to speed quickly. training@intersect.org.au Regular Expressions
Excel for Researchers

Data rarely comes in the form you require. Often it is messy. Sometimes it is incomplete. And sometimes there’s too much of it. Frequently, it has errors. We’ll use one of the most widespread data wrangling tools, Microsoft Excel, to import, sort, filter, copy, protect, transform, summarise,...

Keywords: Excel

Excel for Researchers https://dresa.org.au/materials/excel-for-researchers Data rarely comes in the form you require. Often it is messy. Sometimes it is incomplete. And sometimes there’s too much of it. Frequently, it has errors. We’ll use one of the most widespread data wrangling tools, Microsoft Excel, to import, sort, filter, copy, protect, transform, summarise, merge, and visualise research data. While aimed at novice Excel users, most attendees will walk away with new tricks to work more efficiently with their research data. ‘Clean up’ messy research data Organise, format and name your data Interpret your data (SORTING, FILTERING, CONDITIONAL FORMATTING) Perform calculations on your data using functions (MAX, MIN, AVERAGE) Extract significant findings from your data (PIVOT TABLE, VLOOKUP) Manipulate your data (convert data format, work with DATES and TIMES) Create graphs and charts to visualise your data (CHARTS) Handy tips to speed up your work In order to participate, attendees must have a licensed copy of Microsoft Excel installed on their computer. Speak to your local university IT or Research Office for assistance in obtaining a license and installing the software.   training@intersect.org.au Excel
From PC to Cloud or High Performance Computing

Most of you would have heard of Cloud and High Performance Computing (HPC), or you may already be using it. HPC is not the same as cloud computing. Both technologies differ in a number of ways, and have some similarities as well.

We may refer to both types as “large scale computing” – but...

Keywords: HPC

From PC to Cloud or High Performance Computing https://dresa.org.au/materials/from-pc-to-cloud-or-high-performance-computing Most of you would have heard of Cloud and High Performance Computing (HPC), or you may already be using it. HPC is not the same as cloud computing. Both technologies differ in a number of ways, and have some similarities as well. We may refer to both types as “large scale computing” – but what is the difference? Both systems target scalability of computing, but in different ways. This webinar will give a good overview to the researchers thinking to make a move from their local computer to Cloud of High Performance Computing Cluster. Introduction HPC vs Cloud computing When to use HPC When to use the Cloud The Cloud – Pros and Cons HPC – Pros and Cons The webinar has no prerequisites. training@intersect.org.au HPC
Data Manipulation and Visualisation in Python

Python has deservedly become a popular language for scientific computing. It has all the friendly features and conveniences you’d expect of a modern programming language, and also a rich set of libraries for working with data.

In this workshop, you will explore DataFrames in depth (using...

Keywords: Python

Data Manipulation and Visualisation in Python https://dresa.org.au/materials/data-manipulation-and-visualisation-in-python Python has deservedly become a popular language for scientific computing. It has all the friendly features and conveniences you’d expect of a modern programming language, and also a rich set of libraries for working with data. In this workshop, you will explore DataFrames in depth (using the pandas library), learn how to manipulate, explore and get insights from your data (Data Manipulation), as well as how to deal with missing values and how to combine multiple datasets. You will also explore different types of graphs and learn how to customise them using two of the most popular plotting libraries in Python, matplotlib and seaborn (Data Visualisation). We teach using Jupyter notebooks, which allow program code, results, visualisations and documentation to be blended seamlessly. Perfect for sharing insights with others while producing reproducible research. Join us for this live coding workshop where we write programs that produce results, using the researcher-focused training modules from the highly regarded Software Carpentry Foundation. Working with pandas DataFrames Indexing, slicing and subsetting in pandas DataFrames Missing data values Combine multiple pandas DataFrames Using the Grammar of Graphics to convert data into figures using the seaborn and matplotlib libraries Configuring plot elements within seaborn and matplotlib Exploring different types of plots using seaborn Either \Learn to Program: Python\ or \Learn to Program: Python\ and \Python for Research\ needed to attend this course. If you already have experience with programming, please check the topics covered in the \Learn to Program: Python\ and \Python for Research\ courses to ensure that you are familiar with the knowledge needed for this course. training@intersect.org.au Python
Introduction to Machine Learning using Python: Classification

Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore...

Keywords: Python

Introduction to Machine Learning using Python: Classification https://dresa.org.au/materials/introduction-to-machine-learning-using-python-classification Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the Python programming language and its scientific computing libraries. Comprehensive introduction to Machine Learning models and techniques such as Logistic Regression, Decision Trees and Ensemble Learning. Know the differences between various core Machine Learning models. Understand the Machine Learning modelling workflows. Use Python and scikit-learn to process real datasets, train and apply Machine Learning models. Either \Learn to Program: Python\, \Data Manipulation in Python\ and \Introduction to ML using Python: Introduction & Linear Regression\ or \Learn to Program: Python\, \Data Manipulation and Visualisation in Python\ and \Introduction to ML using Python: Introduction & Linear Regression\ needed to attend this course.  If you already have experience with programming, please check the topics covered in courses above to ensure that you are familiar with the knowledge needed for this course, such as good understanding of Python syntax, basic programming concepts and familiarity with Pandas, Numpy and Seaborn libraries, and basic understanding of Machine Learning and Model Training. Maths knowledge is not required. However, there is a few Math formula covered in this course and the references will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them. training@intersect.org.au Python
Getting started with HPC using PBS Pro

Is your computer’s limited power throttling your research ambitions? Are your analysis scripts pushing your laptop’s processor to its limits? Is your software crashing because you’ve run out of memory? Would you like to unleash to power of the Unix command line to automate and run your analysis...

Keywords: HPC

Getting started with HPC using PBS Pro https://dresa.org.au/materials/getting-started-with-hpc-using-pbs-pro Is your computer’s limited power throttling your research ambitions? Are your analysis scripts pushing your laptop’s processor to its limits? Is your software crashing because you’ve run out of memory? Would you like to unleash to power of the Unix command line to automate and run your analysis on supercomputers that you can access for free? High-Performance Computing (HPC) allows you to accomplish your analysis faster by using many parallel CPUs and huge amounts of memory simultaneously. This course provides a hands on introduction to running software on HPC infrastructure using PBS Pro. Connect to an HPC cluster Use the Unix command line to operate a remote computer and create job scripts Submit and manage jobs on a cluster using a scheduler Transfer files to and from a remote computer Use software through environment modules Use parallelisation to speed up data analysis Access the facilities available to you as a researcher This is the PBS Pro version of the Getting Started with HPC course. This course assumes basic familiarity with the Bash command line environment found on GNU/Linux and other Unix-like environments. To come up to speed, consider taking our \Unix Shell and Command Line Basics\ course. training@intersect.org.au HPC
Introduction to Machine Learning using Python: SVM & Unsupervised Learning

Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore...

Keywords: Python

Introduction to Machine Learning using Python: SVM & Unsupervised Learning https://dresa.org.au/materials/introduction-to-machine-learning-using-python-svm-unsupervised-learning Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the Python programming language and its scientific computing libraries. Comprehensive introduction to Machine Learning models and techniques such as Support Vector Machine, K-Nearest Neighbor and Dimensionality Reduction. Know the differences between various core Machine Learning models. Understand the Machine Learning modelling workflows. Use Python and scikit-learn to process real datasets, train and apply Machine Learning models. Either \Learn to Program: Python\, \Data Manipulation in Python\ and \Introduction to ML using Python: Introduction & Linear Regression\ or \Learn to Program: Python\, \Data Manipulation and Visualisation in Python\ and \Introduction to ML using Python: Introduction & Linear Regression\ needed to attend this course.  If you already have experience with programming, please check the topics covered in courses above to ensure that you are familiar with the knowledge needed for this course, such as good understanding of Python syntax, basic programming concepts and familiarity with Pandas, Numpy and Seaborn libraries, and basic understanding of Machine Learning and Model Training. Maths knowledge is not required. However, there is a few Math formula covered in this course and the references will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them. training@intersect.org.au Python
Getting started with HPC using Slurm

Is your computer’s limited power throttling your research ambitions? Are your analysis scripts pushing your laptop’s processor to its limits? Is your software crashing because you’ve run out of memory? Would you like to unleash to power of the Unix command line to automate and run your analysis...

Keywords: HPC

Getting started with HPC using Slurm https://dresa.org.au/materials/getting-started-with-hpc-using-slurm Is your computer’s limited power throttling your research ambitions? Are your analysis scripts pushing your laptop’s processor to its limits? Is your software crashing because you’ve run out of memory? Would you like to unleash to power of the Unix command line to automate and run your analysis on supercomputers that you can access for free? High-Performance Computing (HPC) allows you to accomplish your analysis faster by using many parallel CPUs and huge amounts of memory simultaneously. This course provides a hands on introduction to running software on HPC infrastructure using Slurm. Connect to an HPC cluster Use the Unix command line to operate a remote computer and create job scripts Submit and manage jobs on a cluster using a scheduler Transfer files to and from a remote computer Use software through environment modules Use parallelisation to speed up data analysis Access the facilities available to you as a researcher This is the Slurm version of the Getting Started with HPC course. This course assumes basic familiarity with the Bash command line environment found on GNU/Linux and other Unix-like environments. To come up to speed, consider taking our \Unix Shell and Command Line Basics\ course. training@intersect.org.au HPC
Data Visualisation in Python

Course Materials

Using the Grammar of Graphics to convert data into figures using the seaborn and matplotlib libraries

Configuring plot elements within seaborn and matplotlib

Exploring different types of...

Keywords: Python

Data Visualisation in Python https://dresa.org.au/materials/data-visualisation-in-python [Course Materials](https://intersectaustralia.github.io/training/PYTHON203/sources/Data-Adv_Python.zip) Using the Grammar of Graphics to convert data into figures using the seaborn and matplotlib libraries Configuring plot elements within seaborn and matplotlib Exploring different types of plots using seaborn Either \Learn to Program: Python\ or \Learn to Program: Python\ and \Python for Research\ needed to attend this course. If you already have experience with programming, please check the topics covered in the \Learn to Program: Python\ and \Python for Research\ courses to ensure that you are familiar with the knowledge needed for this course. We also strongly recommend attending the \Data Manipulation in Python\. training@intersect.org.au Python
Introduction to Machine Learning using Python: Introduction & Linear Regression

Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore...

Keywords: Python

Introduction to Machine Learning using Python: Introduction & Linear Regression https://dresa.org.au/materials/introduction-to-machine-learning-using-python-introduction-linear-regression Machine Learning (ML) is a new way to program computers to solve real world problems. It has gained popularity over the last few years by achieving tremendous success in tasks that we believed only humans could solve, from recognising images to self-driving cars. In this course, we will explore the fundamentals of Machine Learning from a practical perspective with the help of the Python programming language and its scientific computing libraries. Understand the difference between supervised and unsupervised Machine Learning. Understand the fundamentals of Machine Learning. Comprehensive introduction to Machine Learning models and techniques such as Linear Regression and Model Training. Understand the Machine Learning modelling workflows. Use Python and scikit-learn to process real datasets, train and apply Machine Learning models Either \Learn to Program: Python\ and \Data Manipulation in Python\ or \Learn to Program: Python\ and \Data Manipulation and Visualisation in Python\ needed to attend this course.  If you already have experience with programming, please check the topics covered in courses above to ensure that you are familiar with the knowledge needed for this course, such as good understanding of Python syntax and basic programming concepts and familiarity with Pandas, Numpy and Seaborn libraries. Maths knowledge is not required. However, there is a few Math formula covered in this course and the references will be provided. Having an understanding of the Mathematics behind each Machine Learning algorithms is going to make you appreciate the behaviour of the model and know its pros/cons when using them. training@intersect.org.au Python