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  • WORKSHOP: Single cell RNAseq analysis in R

    22 - 23 August 2022

    WORKSHOP: Single cell RNAseq analysis in R https://tess.elixir-europe.org/events/workshop-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](https://satijalab.org/seurat/index.html) - 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. **Lead trainers:** Dr Sarah Williams, Senior Bioinformatician, QCIF Mr Nick Matigan, Biostatistician and Bioinformatician, QCIF Dr Ahmed Mehdi, Senior Biostatistician, QCIF **Format** This online workshop will take place over two half-day sessions. You must attend both sessions. Expert trainers will guide you through each of the topics and provide activities to help you put your new skills into action. **Date/Time:** 22 and 23 August 2022, 1-5pm AEST/ ACST/AWST **Location:** Online **Learning outcomes:** By the end of the workshop you should be able to: 1. Load gene counts into a Seurat format 2. Perform QC and select cells for further analysis 3. Filter and normalise scRNAseq data 4. Cluster cells and identify cluster markers 5. Visualise scRNAseq expression data **Who the workshop is for:** This workshop is for Australian researchers who have or will work on scRNAseq data as part of their projects. You must be associated with an Australian organisation for your application to be considered. This workshop will not teach you the basics of R. While you don’t need to be an expert, you require some basic familiarity with R. For example you should be able to work with tables of data, know how to load an R package, make basic plots (ideally with ggplot2). You should also have basic knowledge of single cell RNA sequencing technology. **How to apply:** This workshop is free but participation is subject to application with selection. Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful). Successful applicants will be provided with a Zoom meeting link closer to the date. Applications close at **11:59pm AEDT, Wednesday 10 August 2022**. **[Apply here](https://biocommons-scrnaseq.eventbrite.com.au/)** _This workshop is presented by the[ Australian BioCommons](https://www.biocommons.org.au/) and[ Queensland Cyber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the assistance of a network of facilitators from the national[ Bioinformatics Training Cooperative](https://www.biocommons.org.au/training-cooperative)._ _This event is part of a series of[ bioinformatics training events](https://www.biocommons.org.au/events). If you'd like to hear when registrations open for other events, please[ subscribe](https://www.biocommons.org.au/subscribe) to Australian BioCommons_ 2022-08-22 13:00:00 UTC 2022-08-23 17:00:00 UTC Australian BioCommons RNA-Seq Australian Biocommons training@biocommons.org.au [] [] 80 workshops_and_courses registration_of_interest Single Cell technologiesscRNAseqSeuratR software
  • WEBINAR: Getting started with whole genome mapping and variant calling on the command line

    24 August 2022

    WEBINAR: Getting started with whole genome mapping and variant calling on the command line https://tess.elixir-europe.org/events/webinar-getting-started-with-whole-genome-mapping-and-variant-calling-on-the-command-line Life scientists are increasingly using whole genome sequencing (WGS) to ask and answer research questions across the tree of life. Before any of this work can be done, there is the essential but challenging task of processing raw sequencing data. Processing WGS data is a computationally challenging, multi-step process used to create a map of an individual’s genome and identify genetic variant sites. The tools you use in this process and overall workflow design can look very different for different researchers, it all depends on your dataset and the research questions you’re asking. Luckily, there are lots of existing WGS processing tools and pipelines out there, but knowing where to start and what your specific needs are is hard work, no matter how experienced you are. In this webinar we will walk through the essential steps and considerations for researchers who are running and building reproducible WGS mapping and variant calling pipelines at the command line interface. We will discuss how to choose and evaluate a pipeline that is right for your dataset and research questions, and how to get access to the compute resources you need. **Who the webinar is for** This webinar is intended for life scientists who are using and building whole genome sequencing mapping and variant calling pipelines. Some familiarity with the concepts of whole genome sequencing is recommended. **Presenter:** Dr Georgina Samaha, Sydney Informatics Hub, University of Sydney **Date/time:** 24 August 2021 - 12:00-13:00 AEST / 11:30 - 12:30 ACST / 10:00-11:00 AWST **How to join:** This webinar is free to join but you must register for a place in advance. **[Register here] (https://unimelb.zoom.us/webinar/register/WN_ekHib2_2QYazaH06VFMPgQ)** 2022-08-24 12:00:00 UTC 2022-08-24 13:00:00 UTC Australian BioCommons Whole genome sequencing Sequencing Genomics Bioinformatics Workflows Australian Biocommons training@biocommons.org.au [] [] 500 workshops_and_courses first_come_first_served []

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