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Keywords: R software  or digital research skills tra... 

Tutorials to learn how to use STAN

Stan tutorials offer links to exceptional tutorial papers, videos and statistics to learn Bayesian statistical methods and applied statistics.

Keywords: Statistics, applied statistics, Bayesian statistics, R software, Python, MATLAB

Tutorials to learn how to use STAN https://dresa.org.au/materials/tutorials-to-learn-how-to-use-stan Stan tutorials offer links to exceptional tutorial papers, videos and statistics to learn Bayesian statistical methods and applied statistics. https://mc-stan.org/about/team/ Statistics, applied statistics, Bayesian statistics, R software, Python, MATLAB
Species Distribution Modelling in R

This set of scripts and videos provide an introduction to running SDMs in R and include some steps to consider that go beyond what's available in the EcoCommons SDM point-and-click tools.

Five videos include: 1. An introduction to SDM in R, 2. occurrence data, 3. environmental data, 4. fitting...

Keywords: Species Distribution Modelling, Ecology, R software, EcoCommons

Species Distribution Modelling in R https://dresa.org.au/materials/species-distribution-modelling-in-r This set of scripts and videos provide an introduction to running SDMs in R and include some steps to consider that go beyond what's available in the EcoCommons SDM point-and-click tools. Five videos include: 1. An introduction to SDM in R, 2. occurrence data, 3. environmental data, 4. fitting your model, 5. model evaluation Scripts and files are available here: https://github.com/EcoCommons-Australia/educational_material/tree/main/SDMs_in_R/Scripts Scripts for all four modules are here: https://www.ecocommons.org.au/wp-content/uploads/EcoCommons_steps_1_to_4.html https://www.ecocommons.org.au/contact/ Species Distribution Modelling, Ecology, R software, EcoCommons ugrad mbr phd
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: R: fundamental skills for biologists

This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.

 

Event description

Biologists need data analysis skills to be able to...

Keywords: Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation

WORKSHOP: R: fundamental skills for biologists https://dresa.org.au/materials/workshop-r-fundamental-skills-for-biologists-81aa00db-63ad-4962-a7ac-b885bf9f676b This record includes training materials associated with the Australian BioCommons workshop ‘R: fundamental skills for biologists’. This workshop took place over four, three-hour sessions on 1, 8, 15 and 22 June 2022.   Event description Biologists need data analysis skills to be able to interpret, visualise and communicate their research results. While Excel can cover some data analysis needs, there is a better choice, particularly for large and complex datasets.  R is a free, open-source software and programming language that enables data exploration, statistical analysis, visualisation and more. The large variety of R packages available for analysing biological data make it a robust and flexible option for data of all shapes and sizes.  Getting started can be a little daunting for those without a background in statistics and programming. In this workshop we will equip you with the foundations for getting the most out of R and RStudio, an interactive way of structuring and keeping track of your work in R. Using biological data from a model of influenza infection, you will learn how to efficiently and reproducibly organise, read, wrangle, analyse, visualise and generate reports from your data in R. Topics covered in this workshop include: Spreadsheets, organising data and first steps with R Manipulating and analysing data with dplyr Data visualisation Summarized experiments and getting started with Bioconductor   This workshop is presented by the Australian BioCommons and Saskia Freytag from WEHI  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): A breakdown of the topics and timings for the workshop Recommended resources (PDF): A list of resources recommended by trainers and participants Q_and_A(PDF): Archive of questions and their answers from the workshop Slack Channel. Materials shared elsewhere:   This workshop follows the tutorial ‘Introduction to data analysis with R and Bioconductor’ which is publicly available. https://saskiafreytag.github.io/biocommons-r-intro/ This is derived from material produced as part of The Carpentries Incubator project https://carpentries-incubator.github.io/bioc-intro/ Melissa Burke (melissa@biocommons.org.au) Bioinformatics, Analysis, Statistics, R software, RStudio, Data visualisation
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
Digital research skills trainer certification guide

This guide to certification is for those who currently design, develop and deliver training as full-time trainers or where training is part of their role, and for those who are considering becoming a skills trainer.

Keywords: digital research skills training, trainer certification, training material

Digital research skills trainer certification guide https://dresa.org.au/materials/digital-research-skills-trainer-certification-guide-b70e3945-8ef1-4cc1-8963-3169bcfe0109 This guide to certification is for those who currently design, develop and deliver training as full-time trainers or where training is part of their role, and for those who are considering becoming a skills trainer. contact@ardc.edu.au digital research skills training, trainer certification, training material
Guide to designing digital research skills training materials: textual materials

The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Textual Materials aims to support training materials creators, trainers and national training infrastructure providers in the creation of textual guides while also encouraging the sharing...

Keywords: digital research skills training, learning design, textual training materials, training material

Guide to designing digital research skills training materials: textual materials https://dresa.org.au/materials/guide-to-designing-digital-research-skills-training-materials-textual-materials-8b685c24-0362-4cc9-9908-63227ecf0e0f The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Textual Materials aims to support training materials creators, trainers and national training infrastructure providers in the creation of textual guides while also encouraging the sharing and reuse of their training materials. It aims to facilitate the design, development and delivery of textual guides on digital research and data skills in alignment with best practices in learning and training. This tool is informed by the Universal Design for Learning principles which aims to eliminate barriers in the design of learning materials to make content accessible to all. contact@ardc.edu.au digital research skills training, learning design, textual training materials, training material
Guide to designing digital research skills training materials: presentations and videos

The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Presentations and Videos aims to support training materials creators, trainers and national training infrastructure providers in the design and delivery of presentations and videos while...

Keywords: digital research skills training, learning design, training presentations, training videos, training material

Guide to designing digital research skills training materials: presentations and videos https://dresa.org.au/materials/guide-to-designing-digital-research-skills-training-materials-presentations-and-videos-8d8c091b-c719-4200-874a-eb05a81bc49a The Australian Research Data Commons (ARDC) Guide to Designing Digital Research Skills Training Materials: Presentations and Videos aims to support training materials creators, trainers and national training infrastructure providers in the design and delivery of presentations and videos while also encouraging the sharing and reuse of their training materials. It aims to facilitate the design, development and delivery of digital research and data skills videos and presentations in alignment with best practices for learning and training.  This tool is informed by the Universal Design for Learning framework, which aims to eliminate barriers in the design of learning materials and make content accessible to all. contact@ardc.edu.au digital research skills training, learning design, training presentations, training videos, training material
VOSON Lab Code Blog

The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages.

Keywords: visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics

Resource type: tutorial, other

VOSON Lab Code Blog https://dresa.org.au/materials/voson-lab-code-blog The VOSON Lab Code Blog is a space to share methods, tips, examples and code. Blog posts provide techniques to construct and analyse networks from various API and other online data sources, using the VOSON open-source software and other R based packages. robert.ackland@anu.edu.au visualisation, Data analysis, data collections, R software, Social network analysis, social media data, Computational Social Science, quantitative, Text Analytics researcher support phd masters