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Authors: Harrison, Paul (orcid: 0000...  or ARDC 

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
ARDC digital research capabilities and skills framework

This informational flyer outlines the value of skills frameworks and describes at a high level the various elements of the ARDC's Capabilities and Skills Framework.

Capabilities and Skills Landscape
Glossary - Framework terminology
Data and Digital Research roles
Skills/Role...

Keywords: training material, skills framework, ARDC skills framework, ARDC capabilities framework, national skills framework

ARDC digital research capabilities and skills framework https://dresa.org.au/materials/ardc-digital-research-capabilities-and-skills-framework-3b376311-87dd-470f-bb8d-e99459434c97 This informational flyer outlines the value of skills frameworks and describes at a high level the various elements of the ARDC's Capabilities and Skills Framework. Capabilities and Skills Landscape Glossary - Framework terminology Data and Digital Research roles Skills/Role profiles Learning paths Skills/Data roles matrix contact@ardc.edu.au Savill, Jo (type: Editor) Duncan, Ian (type: Editor) Unsworth, Kathryn (type: Editor) Murphy, Paul (type: Editor) training material, skills framework, ARDC skills framework, ARDC capabilities framework, national skills framework
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