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Authors: Harrison, Paul (orcid: 0000...  or Papaioannou, Anastasios (or... 

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
DReSA: Project team reflections

This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual...

Keywords: training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training

DReSA: Project team reflections https://dresa.org.au/materials/dresa-project-team-reflections-9dcb8538-6b7c-4822-b0ee-fbe57085dc70 This presentation provides thoughts and reflections from the Digital Research Skills Australaisa (DReSA) project team on DReSA. Team members highlight their perspectives on value propositions and benefits for their respective institutiosn/organisations and nationally, as well as individual reflections on collaboration and working together on the project so far. You can watch the video on YouTube here: https://youtu.be/qqH92itI8SI   contact@ardc.edu.au training events, training material, training repository, skilled workforce, digital research skills, digital research training, digital research, trainers, FAIR training
Intersect: Training portfolio

This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows,...

Keywords: training impact, evaluation, short-term evaluation, long-term evaluation, behavioural change, survey design, skills training, training material

Intersect: Training portfolio https://dresa.org.au/materials/intersect-training-portfolio-8c82060d-5eea-4091-af7b-396c9c073dab This presentation explores Intersect's training evaluation model. Short term evaluation for immediate satisfaction and value of the training. Long term evaluation methods with a specific survey design to determine behavioural change and impact over time of the training on researchers' workflows, use of support services post training and looking for links between digital tools/technologies training and research outputs and grants. You can watch the full video on YouTube here: https://youtu.be/J3tCC-t_eO4 contact@ardc.edu.au training impact, evaluation, short-term evaluation, long-term evaluation, behavioural change, survey design, skills training, training material
Skills training & materials - developing sharing guidelines and agreements

Anyone who has developed training content - specifically hands-on, short format, data science training - will know that it is expensive and time consuming. As a rule of thumb, one can expect to spend 15-20 hours of development time per hour of delivery time.

Even once the main work is done,...

Keywords: training material, training, sharing guidelines, sharing agreements

Skills training & materials - developing sharing guidelines and agreements https://dresa.org.au/materials/skills-training-materials-developing-sharing-guidelines-and-agreements-3bd2409c-44d0-45d9-b598-e3301242fb2d Anyone who has developed training content - specifically hands-on, short format, data science training - will know that it is expensive and time consuming. As a rule of thumb, one can expect to spend 15-20 hours of development time per hour of delivery time. Even once the main work is done, there are still ongoing maintenance demands, from correcting the inevitable typos and adapting to software version updates, to major rewrites as best practice techniques evolve. Few Australians training organisations have a funding mandate for developing training material for general use. Instead most of us build training for our own communities in response to demand from those communities, allocating our limited resources to the areas of perceived highest demand. Notwithstanding this local focus, most training organisations operate in similar research environments with similar community demands, so there are real opportunities for benefit from collaboration between those organisations. In this session we will discuss how such collaboration could occur and whether a standardised national agreement around sharing of training material is an achievable outcome. This session will not discuss co-delivery opportunities, institution-specific content such as HPC training and data management, or consolidation of existing similar workshops into a single course. These are important topics, but we don’t have time to do them justice today. contact@ardc.edu.au training material, training, sharing guidelines, sharing agreements
National skills ecosystem - call to action

In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4.

  • Skilled trainers / facilitators

  • National training registry

  • National training event calendar

  • Jointly developed training

  • Research...

Keywords: national skills initiatives, data skills, training, skills community, training material

National skills ecosystem - call to action https://dresa.org.au/materials/national-skills-ecosystem-call-to-action-ffd9b4ed-b557-496b-ac35-72467c03c71b In this Community Action session working groups will be formed based on the challenges/opportunities that were prioritised in Community Action session #4. - Skilled trainers / facilitators - National training registry - National training event calendar - Jointly developed training - Research support professionals: career/progression contact@ardc.edu.au national skills initiatives, data skills, training, skills community, training material