Workshops
Single cell RNAseq analysis in R
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 introductory online workshop is offered nationally free of charge by the Australian BioCommons and QCIF. As a member of the Bioinformatics Training Cooperative, Melbourne Bioinformatics is contributing expert facilitators from the University of Melbourne. Places are limited. Applications close 11:59pm AEDT, 10 August 2022.
Workshops
Introduction to Galaxy and Galaxy workflows
Don’t like the command line? Use Galaxy.
Workshop Description:
This beginners tutorial will introduce Galaxy’s interface, tool use, histories. Click on these links to learn about Galaxy and available training material. The material covered in this workshop is freely available at this link. Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis. Finally, it allows users to share and publish analyses via the web.Workshops
Sequencing read QC using Galaxy
Learn how to perform QC on raw sequencing reads using the Galaxy interface
Workshop Description:
This beginners tutorial will teach you how to use the Galaxy’s interface to perform quality control of raw long and short read sequencing data. The material covered in this workshop is freely available at this link. Galaxy is an open source, web-based platform for accessible, reproducible, and transparent computational biomedical research. It allows users without programming experience to easily specify parameters and run individual tools as well as larger workflows. It also captures run information so that any user can repeat and understand a complete computational analysis. Finally, it allows users to share and publish analyses via the web.Webinar
Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud
Bioinformatics workflows can support portable, reproducible and scalable analysis of omics datasets but using workflows can be challenging for both beginners and experienced bioinformaticians. Beginners face a steep learning curve to be able to build and deploy their own bioinformatics workflows while those with more experience face challenges productionising and scaling code for custom workflows and big data.
Bioinformaticians across the world are using Nextflow to build and manage workflows. Many of these workflows are shared for others to use and supported by the community via nf-co.re. So far, 39 workflows for omics data are available with another 23 under development. These workflows cover common analyses such as RNAseq, mapping, variant calling, single cell transcriptomics and more and can be easily deployed by anyone, regardless of skill level.
Workshops
RNA-Seq: reads to differential genes and pathways
RNA sequencing (RNA-seq) is a common method used to understand the differences in gene expression and molecular pathways between two or more groups. This workshop introduces the fundamental concepts of RNA sequencing experiments and will allow you to try out the analysis using data from a study of Williams-Beuren Syndrome, a rare disease.
In the first part of the workshop you will learn how to convert sequence reads into analysis ready count data. To do this we will use nf-core/rnaseq – a portable, scalable, reproducible and publicly available workflow on Pawsey Nimbus Cloud. In the second part of the workshop you will use the count data you created to identify differential genes and pathways using R/Rstudio. By the end of the workshop, you should be able to perform your own RNA-seq analysis for differential gene expression and pathway analysis!
(more…)Workshops
Introduction to R for Biologists
Ever wanted to visualise your own data? You can with R!
Workshop Description:
This workshop has been developed collaboratively by training specialists at Peter MacCallum Cancer Center and Melbourne Bioinformatics and is freely available at this link. This introduction to R and RStudio will provide beginners with experience with loading, manipulating and visualising biological data using the tidyverse collection of R packages. The example data used is publicly available RNA-seq data, therefore attendees will gain experience in the structure and appearance of RNA-seq data. (more…)Workshops
Command line skills in UNIX
A hands-on workshop covering the basics of the Unix/Linux command line interface.
Workshop Description:
Knowledge of the Unix operating system is fundamental to the use of many popular bioinformatics command-line tools. Whether you choose to run your analyses locally or on an HPC system, knowing your way around a command-line interface is highly valuable. This workshop will introduce you to Unix concepts by way of a series of hands-on exercises.Completion of this workshop will provide the background knowledge required for other Melbourne Bioinformatics workshops that require command-line skills.
Workshops
QIIME2 analysis of bacterial 16s rRNA
This workshop will give you an introduction to the QIIME2 analysis platform using 16S rRNA amplicon data from coral-associated bacteria.
Workshop date: Thursday 6th October 2022
EOI deadline: 5pm Friday 23rd September 2022
Successful applicants notified: Wednesday 28th September 2022 (more…)Workshops
Variant calling using GATK4 command line workflow
Workshop date: Wednesday 19th October
EOI deadline: 5pm Friday 7th October
Successful applicants notified: Wednesday 12th October (more…)Workshops
Introduction to Workflow languages
This hands on workshop demonstrates how to write workflows using a workflow language.
Workshop Description:
This workshop demonstrates how to write workflows using a workflow language. An introduction to workflow theory, implementation using the CWL language, and execution on a compute environment will be demonstrated. By the end of the session, participants will be able to write and execute basic workflows in CWL. Participants will also gain experience migrating an existing workflow from one system (Galaxy) to another (CWL). Skills learned will be easily transferable to other workflow languages (eg Nextflow) participants may want to learn in the future. Workflow systems have become a core aspect of research over time. Most researchers will run a repeatable analysis requiring multiple software tools during their career. For this reason, skills involving developing, running and maintaining workflows are continuing to be valuable in our industry. A number of workflow systems are currently popular, including Galaxy, CWL, WDL and Nextflow. While Galaxy is the easiest system to get started with, it is not suitable for all workflows and all data. In these cases, researchers may need to use a dedicated workflow language, rather than a system like Galaxy. A few examples:- Galaxy server does not permit certain data being run (sensitive data)
- Galaxy server does not have required software tool installed, and would be highly time consuming to develop a wrapper
- Galaxy server may not offer the required amount compute resources