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DTSTAMP:20261016T062402Z
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DTSTART:20261208T090000Z
DTEND:20261210T170000Z
DESCRIPTION:## Overview\n\nSpatial transcriptomics is a rapidly evolving te
 chnology that allows researchers to study gene expression within the spati
 al context of tissue architecture. This course provides a practical introd
 uction to the analysis of both sequencing-based and imaging-based spatiall
 y resolved transcriptomics (SRT) data\, combining theoretical background w
 ith hands-on exercises using mostly the [R/Bioconductor](https://www.bioco
 nductor.org/) ecosystem. Participants will gain an understanding of experi
 mental design\, data preprocessing\, and downstream analysis workflows. Th
 rough lectures and guided practicals\, the course aims to equip participan
 ts with the skills needed to perform their own spatial transcriptomics ana
 lyses and interpret the results in a biological context.\n\n## Audience\n\
 nThis course is designed for PhD students\, postdoctoral and other researc
 hers in the life sciences from both academia and industry who are seeking 
 to understand and analyze spatial transcriptomics data.\n\n## Learning out
 comes\n\nAt the end of the course\, the participants are expected to:\n\n-
  **Explain** the principles and describe applications of both sequencing-b
 ased and imaging-based spatially-resolved transcriptomics (SRT)\n- **Ident
 ify** potential pitfalls and limitations of SRT experiments and analysis w
 orkflows.\n- **Define** applications for cell segmentation and apply frequ
 ently-used cell segmentation methods\n- **Assess** and interpret raw outpu
 ts and spatial metadata files\, understanding their structure and relevanc
 e for downstream analyses.\n- **Define** important aspects of quality cont
 rol\, feature selection\, dimensionality reduction and differential gene e
 xpression to SRT data and apply those. \n- **Clarify** various spatial sta
 tistics and their application to biological questions.\n- **Use** frequent
 ly-used methods to analyze multi-sample SRT experiments.\n\n## Prerequisit
 es\n\n### Knowledge / competencies\n\n**Participants must have basic knowl
 edge in UNIX\, R\, dimensionality reduction\, clustering and Next-Generati
 on Sequencing (NGS) techniques.**\n\nThis course is part of the [Omics Dat
 a Analysis learning path](https://www.sib.swiss/training/learning-paths?pa
 th=omics-data-analysis). To get the most out of this course\, you should m
 eet the learning outcomes of [Single-Cell Transcriptomics with R](https://
 www.sib.swiss/training/course/ISCTR)\, [Introduction to bulk RNA-Seq: From
  Quality Control to Pathway Analysis](https://www.sib.swiss/training/cours
 e/IRNAS)\, [NGS - Quality control\, Alignment\, Visualisation](https://www
 .sib.swiss/training/course/NGSQC)\, [First Steps with R in Life Sciences](
 https://www.sib.swiss/training/course/FSWRR) and [UNIX Fundamentals](https
 ://www.sib.swiss/training/course/2012_UNIXF). \n\nIn summary\, participant
 s must already have a basic knowledge in:\n\n- Next Generation Sequencing 
 (NGS) techniques\n- Analyzing gene expression data\n- Dimensionality reduc
 tion (PCA\, UMAP)\n- Graph-based clustering \n- R (evaluate your R skills 
 [here](https://docs.google.com/forms/d/e/1FAIpQLSdIyeuabd_ZOWXgI1MWHapmaOM
 u20L9ESkLDZiWnpmkpujyOg/viewform?usp=sf_link))\n- UNIX (self-assess your s
 kills with the e-learning course [UNIX Fundamentals](https://www.sib.swiss
 /training/course/2012_UNIXF)\, and this [quiz](https://docs.google.com/for
 ms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?u
 sp=sf_link))\n\n### Technical\n\nAttendees should have a Wi-Fi enabled com
 puter. An online R and RStudio environment will be provided. However\, in 
 case you wish to perform the practical exercises on your own computer\, pl
 ease take a moment to install R (&gt\; 4.5) and Rstudio before the course.
 \n\n## Schedule – CE(S)T time zone\n\n## Application\n\nThe registration
  fees for academics are **300 CHF** and **1500 CHF** for for-profit compan
 ies.\n\nWhile participants are registered on a first come\, first served b
 asis\, exceptions may be made to ensure diversity and equity\, which may i
 ncrease the time before your registration is confirmed.\n\nApplications wi
 ll close on **01.12.2026** or as soon as the places will be filled up. Can
 cellation after **01.12.2026** will not be reimbursed. Please note that pa
 rticipation in SIB courses is subject to our [general conditions](https://
 www.sib.swiss/legal-documents).\n\nYou will be informed by email of your r
 egistration confirmation. Upon reception of the confirmation email\, parti
 cipants will be asked to confirm attendance by paying the fees within **5 
 working days**.\n\n## Venue and Time\n\nThe course will take place at the 
 University of Lausanne.\n\nThe course will start at 9:00 CET and end aroun
 d 17:00 CET.\n\nPrecise information will be provided to the registered par
 ticipants in due time.\n\n## Additional information\n\nCoordination: Geert
  van Geest\, SIB Training group.\n\nA **Certificate of Attendance** will b
 e sent provided you were present at the course\, whereas a **Certificate o
 f Achievement** recommending 0.75 ECTS will be sent provided you passed th
 e exam.\n\nYou are welcome to register 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\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-eur
 ope.org/events/code-of-conduct). Participants of SIB courses are also requ
 ired to abide by the same code.\n\nFor more information\, please contact [
 training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Introduction to Spatial Transcriptomics Data Analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20261208_ISTDA
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