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Authors: Harrison, Paul (orcid: 0000...  or Monash Partners 

HeSANDA Monash Node User Guides

This guide developed by the HeSANDA Monash node provides an overview for users of Health Data Australia (HDA).
HDA helps researchers discover and access health data. HDA is a registry and does not store the data itself but provides descriptions of the data from data owners' publishing partners....

Keywords: Health Data Australia, health data, data request, HDA, HeSANDA, data access

HeSANDA Monash Node User Guides https://dresa.org.au/materials/hesanda-monash-node-user-guides This guide developed by the HeSANDA Monash node provides an overview for users of Health Data Australia (HDA). HDA helps researchers discover and access health data. HDA is a registry and does not store the data itself but provides descriptions of the data from data owners' publishing partners. Using HDA, researchers can search these descriptions, find data of use to do their research, then request access to it. The request will be sent to the owner of the data to review. Data owners receive email notifications about new data requests and can then log into the HDA Data Request platform to review the request and determine whether access can be granted and then respond to the researcher requesting access. If the request is approved, the owner arranges for the researcher to be given access to the data. The dataset descriptions (‘metadata’) contained on HDA help researchers understand the kinds of data that exist and assess whether a dataset may be of value to their research, without the need to actually access the data. In addition to metadata, data owners provide other documentation describing the data they hold, such as study protocols and data dictionaries. Using HDA, researchers can search for data, save their searches, submit and manage data requests. Amany.Gouda-Vossos@ardc.edu.au Health Data Australia, health data, data request, HDA, HeSANDA, data access
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
HeSANDA Monash Node Workshop Content

Slide presentation for a HeSANDA workshop delivered on January 1, 2023, which provides the audience with a broad understanding of the HeSANDA program, including Health Data Australia (HDA). 
 
What is HeSANDA:
The Health Studies Australian Data Asset (HeSANDA) is a national program that makes...

Keywords: health data, clinical trials, HeSANDA, Health Data Australia

HeSANDA Monash Node Workshop Content https://dresa.org.au/materials/hesanda-monash-node-workshop-content Slide presentation for a HeSANDA workshop delivered on January 1, 2023, which provides the audience with a broad understanding of the HeSANDA program, including Health Data Australia (HDA).    What is HeSANDA: The Health Studies Australian Data Asset (HeSANDA) is a national program that makes health and medical research data easier to find. It facilitates access, sharing and reuse of research data. This results in a reduction in research waste, improvements in researcher collaboration, and an opppotunity ti answer new research questions. It aims to support more efficitent and effective research to help improve health outcome.   Amany.Gouda-Vossos@ardc.edu.au health data, clinical trials, HeSANDA, Health Data Australia