BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260614T183358Z UID:cdd1997f-1466-4799-a776-aac49ab04bc9 DTSTART:20210615T090000Z DTEND:20210617T170000Z DESCRIPTION:**The course is now full with a long waiting list. If you do no t want to miss your chance to be part of the next session and remain infor med about all training activities at SIB\, we highly recommend you to keep an eye on our list of upcoming events (https://www.sib.swiss/training/upc oming-training-courses) and subscribe to our courses mailing list here (if not yet done): https://lists.sib.swiss/mailman/listinfo/courses. Thank yo u for your understanding.**\n\n\n# Overview\n\nIn contrast to the Bulk RNA sequencing used to quantify the abundance of gene and transcript expressi on at a whole population level\, single-cell RNA sequencing (scRNAseq) all ows researchers to study gene expression profile at a single cell resoluti on while enabling the discovery of tissue specific subpopulations and mark ers. For example\, contrasting different sample conditions i.e. disease vs . normal using scRNAseq can help identify sub-cellular differential behavi ours and thus target specific gene markers. This 3-day course will cover t he main technologies as well main aspects to consider while designing a sc RNAseq experiment including a hands-on practical data analysis session app lied to droplet-based methods.\n\n\n# Audience\nThis course is intended fo r life scientists and bioinformaticians familiar with "Next Generation Seq uencing" who want to acquire the necessary skills to analyse scRNA-seq gen e expression data.\n\n# Learning objectives\n\nAt the end of the course\, participants will be able to:\n\n * distinguish advantages and pitfalls o f scRNAseq\n * design their own scRNA-seq experiment\n * apply a downstr eam analysis using R\n \n\n# Knowledge / competencies prerequired (Mandat ory)\n\nParticipants should already have a basic knowledge in Next Generat ion Sequencing (NGS) techniques\, or have already followed the "[NGS - Qua lity control\, Alignment\, Visualisation](https://www.sib.swiss/training/c ourse/2019-06-NGS6)". Knowledge in RNA sequencing is a plus. A basic knowl edge of the R statistical software is required. [Test your R skills with t he quiz here\, before registering](https://docs.google.com/forms/d/e/1FAIp QLSdIyeuabd_ZOWXgI1MWHapmaOMu20L9ESkLDZiWnpmkpujyOg/viewform?usp=sf_link). \n\n\n# Technical requirements\n\nAttendees should have a Wi-Fi enabled la ptop. An online R and RStudio environment will be provided\, but attendees who wish to run the practicals on their own laptop should install [R](htt ps://cran.r-project.org/) and [RStudio](https://rstudio.com/products/rstud io/)\, as well as install the R packages [Seurat](https://cran.r-project.o rg/web/packages/Seurat/index.html)\, [scran](https://bioconductor.org/pack ages/release/bioc/html/scran.html)\, [scater](https://bioconductor.org/pac kages/release/bioc/html/scater.html)\, [SingleR](https://bioconductor.org/ packages/release/bioc/html/SingleR.html) and [monocle](https://bioconducto r.org/packages/release/bioc/html/monocle.html)\, before the start of the c ourse. \n\n# Program\n\n## First day\n\nIntroduction to scRNAseq:\n * Tec hnologies\n * Experimental design\n * R versus GUI-based tools\n\nQualit y control\n * Dropouts - Doublets\n * Doublet removal using simulation\n * Ribosomal / mitochondrial RNAs\n * Cell cycling\n\nNormalization and scalability\n * Feature selection\n * Log scaling\n * Confounding facto rs removal\n\n## Second day\n\nDimensionality reduction and cell type clus tering \n * PCA\n * tSNE\n * UMAP\n * Clustering methods (Hierarchical \, K-means and Graph-based)\n * Data integration of complex experimental designs\n \nCell type identification and marker identification\n * Metho ds and applications\n\nDifferential expression analysis\n * Methods overv iew\n\n## Third day\n\nDifferential expression analysis - continued\n * D E between clusters \n * DE between samples (involving data integration)\n * Gene set enrichment analysis\n\nPseudotime analysis\n * Methods and a pplications\n\n\n# Application\n**The course is now full. Applications wil l be placed on the waiting list. Should a spot become available\, priority will be given to those on the waiting list.**\n\nThe registration fees fo r academics are **180 CHF** and **900 CHF** for for-profit companies.\n\nY ou will be informed by email of your registration confirmation. Upon recep tion of the confirmation email\, participants will be asked to confirm att endance by paying the fees within 5 days.\n\nApplications will close once the places will be filled. Deadline for registration and free-of-charge ca ncellation is set to **01/06/2021**. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject t o our [general conditions](https://www.sib.swiss/training/terms-and-condit ions).\n\n# Venue and Time\nThis course will be streamed. \n\nIt will star t at 9:00 and end around 17:00. \n\nPrecise information will be provided t o the participants in due time.\n\n\n# Additional information\nCoordinati on: Patricia Palagi\n\nWe will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).\n\nYou are welcome to reg ister to the SIB courses mailing list to be informed of all future courses and workshops\, as well as all important deadlines using the form [here]( https://lists.sib.swiss/mailman/listinfo/courses).\n\nPlease note that par ticipation in SIB courses is subject to our [general conditions](https://w ww.sib.swiss/training/terms-and-conditions).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/events/code-of-conduct). Partic ipants of SIB courses are also required to abide by the same code.\n\nFor more information\, please contact [training@sib.swiss](mailto://training@s ib.swiss). LOCATION:SIB SUMMARY:Single-Cell Transcriptomics with R URL;VALUE=URI:https://www.sib.swiss/training/course/20210615_ISCTR END:VEVENT END:VCALENDAR