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 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.

DOI: 10.5281/zenodo.7072910

Licence: Creative Commons Attribution 4.0

Contact: Melissa Burke (melissa@biocommons.org.au)

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


Additional information

Status: Active

Authors: Williams, Sarah, Mehdi, Ahmed (orcid: 0000-0002-9300-2341), Matigan, Nick, Barugahare, Adele (orcid: 0000-0002-8976-0094), Harrison, Paul (orcid: 0000-0002-3980-268X), Morgan, Steven (orcid: 0000-0001-6038-6126), Whitfield, Holly (orcid: 0000-0002-7282-387X)

WORKSHOP: Single cell RNAseq analysis in R https://dresa.org.au/materials/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 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