Planned intervention: On Thursday March 28th 07:00 UTC Zenodo will be unavailable for up to 5 minutes to perform a database upgrade.
Published August 22, 2022 | Version v1
Other Open

WORKSHOP: Single cell RNAseq analysis in R

  • 1. QCIF
  • 2. Monash Bioinformatics Platform
  • 3. Melbourne Bioinformatics
  • 4. University of Melbourne

Description

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.

Files

Event metadata.pdf

Files (5.3 MB)

Name Size Download all
md5:ea2bca73015b2b679fc3edb39334258f
125.0 kB Preview Download
md5:8a8dbd665a892e5163d9067db028bf9e
92.7 kB Preview Download
md5:ad9b8dc5fe6141a4efe79f6493c7e99e
126.4 kB Preview Download
md5:3147ad428e9b1bd5a56ba7299eaa6a0a
86.3 kB Preview Download
md5:141f8554df7c8d4900c8bd200fa63ade
91.4 kB Preview Download
md5:5595a298756703ef9109f41324b9ab86
4.7 MB Preview Download

Additional details