BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260626T161257Z UID:ea8a1a23-6cde-4c7a-9c38-fd95014c6ff1 DTSTART:20231011T030000Z DTEND:20231012T060000Z DESCRIPTION:RNA sequencing (RNAseq) is a popular and powerful technique use d to understand the activity of genes. Using differential gene profiling m ethods\, we can use RNAseq data to gain valuable insights into gene activi ty and identify variability in gene expression between samples to understa nd the molecular pathways underpinning many different traits. \n\nIn this hands-on workshop\, you will learn RNAseq fundamentals as you process\, a nalyse\, and interpret the results from a real RNAseq experiment on the co mmand-line. In session one\, you will convert raw sequence reads to analys is-ready count data with the[ nf-core/rnaseq](https://nf-co.re/rnaseq/usag e) workflow. In session two\, you’ll work interactively in RStudio to id entify differentially expressed genes\,perform functional enrichment analy sis\, and visualise and interpret your results using popular and best prac tice R packages. \n\nThis workshop is being delivered as a part of the Au stralian BioCommons[ Bring Your Own Data Platforms Project](https://www.bi ocommons.org.au/byo-data-platform-expansion) and will provide you with an opportunity to explore services and infrastructure built specifically for life scientists working at the command line. By the end of the workshop\, you will be familiar with[ Pawsey’s Nimbus cloud](https://pawsey.org.au/ systems/nimbus-cloud-service/) platform and be able to process your own RN Aseq datasets and perform differential expression analysis on the command- line. \n\n**Lead Trainers:** \n\nDr Nandan Deshpande\, Senior Research Bi oinformatician\, Sydney Informatics Hub\nDr Georgina Samaha\, Bioinformati cs Group Lead\, Sydney Informatics Hub\n\n**Date/Time:** 11 &\; 12 Octo ber 2023\, 2 - 5pm AEST/1:30 - 4:30pm ACST/12 - 3pm AWST \n\n**Location:** Online\n\n**Format:**\n\nThis online workshop will take place over two th ree-hour sessions. You must attend both sessions to get the most out of th e workshop. Expert trainers will introduce new topics and guide you throug h hands-on activities to help you put your new skills into action. \n\n**L earning outcomes:**\n\nBy the end of the workshop you should be able to:\n \n- List the steps involved in RNAseq data processing and differential exp ression analysis\n- Understand key concepts and considerations for RNAseq experiments \n- Describe the benefits of using nf-core workflows\n- Run th e nf-core/rnaseq workflow to perform:\n - Quality control\n - Read a lignment\n - Read quantification to generate raw counts\n- Use R/RStudi o on to perform:\n - Quality control\n - Identify differentially exp ressed genes \n - Perform functional enrichment/pathway analysis\n\n**W ho the workshop is for:**\n\nThis workshop is for Australian researchers o r bioinformaticians who are new to working with RNAseq datasets on the com mand-line interface and have or will be using bulk RNAseq datasets to iden tify differentially expressed genes as part of their projects. You must be associated with an Australian organisation for your application to be con sidered.\n\nThe workshop will be conducted in a Unix environment and will use R/RStudio. \n\nBasic command line knowledge is required. You must know how to navigate the directory structure and copy files between the comput ers. If you need a refresher on Unix/Linux try[ this online tutorial](http s://linuxjourney.com/lesson/the-shell).\n\nBasic knowledge of R/RStudio is required. You must know how to set up directories\, run commands\, readin g in and outputting files. If you need a refresher on R/RStudio try the[ Introduction to R and RStudio section](https://swcarpentry.github.io/r-nov ice-gapminder/01-rstudio-intro.html) of this online tutorial.\n\nIt’s re commended that you watch the following webinars before joining the worksho p:\n\n- [Getting started with RNAseq: Transforming raw reads into biologic al insights](https://www.biocommons.org.au/events/rnaseqwebinar)\n- [Porta ble\, reproducible and scalable bioinformatics workflows using Nextflow an d Pawsey Nimbus Cloud](https://youtu.be/VnLX63yXbJU).\n\n**How to apply:** \n\n**[Apply here](https://www.eventbrite.com.au/e/rna-seq-reads-to-differ ential-genes-and-pathways-tickets-677905422367)**\n\nThis workshop is free but participation is subject to application with selection. \n\n**_Applic ations close at 11:59pm AEST\, Monday 25 September 2023._**\n\nApplication s will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful\, waiting list\, u nsuccessful). Successful applicants will be provided with a Zoom meeting l ink closer to the date.\n\nMore information on the selection process is pr ovided in our[ Advice on applying for Australian BioCommons workshops.](ht tps://www.biocommons.org.au/workshop-applications)\n\n**[Apply here](https ://www.eventbrite.com.au/e/rna-seq-reads-to-differential-genes-and-pathway s-tickets-677905422367)**\n\n_This workshop is presented by the[ Australia n BioCommons](https://www.biocommons.org.au/)\,[ Sydney Informatics Hub](h ttps://www.sydney.edu.au/research/facilities/sydney-informatics-hub.html) and[ Pawsey Supercomputing Research Centre](https://pawsey.org.au/) with t he assistance of a network of facilitators from the national[ Bioinformati cs Training Cooperative](https://www.biocommons.org.au/training-cooperativ e)._\n\n_This event is part of a series of[ bioinformatics training events ](https://www.biocommons.org.au/events). If you'd like to hear when regist rations open for other events\, please[ subscribe](https://www.biocommons. org.au/subscribe) to Australian BioCommons._ SUMMARY:WORKSHOP: RNASeq: reads to differential genes and pathways URL;VALUE=URI:https://www.biocommons.org.au/events/rnaseq2023 END:VEVENT END:VCALENDAR