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DTSTAMP:20260407T174635Z
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DTSTART:20260603T090000Z
DTEND:20260605T170000Z
DESCRIPTION:## Overview\nSpatial transcriptomics is a rapidly evolving tech
 nology that allows researchers to study gene expression within the spatial
  context of tissue architecture. This course provides a practical introduc
 tion to the analysis of both sequencing-based and imaging-based spatially 
 resolved transcriptomics (SRT) data\, combining theoretical background wit
 h 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\nT
 his course is designed for PhD students\, postdoctoral and other researche
 rs in the life sciences from both academia and industry who are seeking to
  understand and analyze spatial transcriptomics data.\n\n## Learning outco
 mes\nAt the end of the course\, the participants are expected to:\n\n- Exp
 lain the principles and describe applications of both sequencing-based and
  imaging-based spatially-resolved transcriptomics (SRT)\n- Identify potent
 ial pitfalls and limitations of SRT experiments and analysis workflows.\n-
  Define applications for cell segmentation and apply frequently-used cell 
 segmentation methods\n- Assess and interpret raw outputs and spatial metad
 ata files\, understanding their structure and relevance for downstream ana
 lyses.\n- Define important aspects of quality control\, feature selection\
 , dimensionality reduction and differential gene expression to SRT data an
 d apply those. \n- Clarify various spatial statistics and their applicatio
 n to biological questions.\n- Use frequently-used methods to analyze multi
 -sample SRT experiments.\n\n## Prerequisites\n\n### Knowledge / competenci
 es\n\nYou should meet the learning outcomes of [Single-Cell Transcriptomic
 s with R](https://www.sib.swiss/training/course/20241112_ISCTR)\n\nIn summ
 ary\, participants must already have a basic knowledge in:\n\n- Next Gener
 ation Sequencing (NGS) techniques\n- Analyzing gene expression data\n- Dim
 ensionality reduction (PCA\, UMAP)\n- Graph-based clustering \n- `R` (eval
 uate your `R` skills [here](https://docs.google.com/forms/d/e/1FAIpQLSdIye
 uabd_ZOWXgI1MWHapmaOMu20L9ESkLDZiWnpmkpujyOg/viewform?usp=sf_link))\n- `UN
 IX` (self-assess your skills with the e-learning course [`UNIX` Fundamenta
 ls](https://www.sib.swiss/training/course/2012_UNIXF)\, and this [quiz](ht
 tps://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBi
 aqcaHoBKNB27MQ/viewform?usp=sf_link))\n\n\n### Technical\n\nAttendees shou
 ld have a Wi-Fi enabled computer. An online R and RStudio environment will
  be provided. However\, in case you wish to perform the practical exercise
 s on your own computer\, please take a moment to install R (&gt\; 4.5) and
  Rstudio before the course.\n\n## Schedule - CET time zone\n\n## Applicati
 on\n\n\nThe registration fees for academics are **CHF 300** and **CHF 1500
 ** for for-profit companies. While participants are registered on a first 
 come\, first served basis\, exceptions may be made to ensure diversity and
  equity\, which may increase the time before your registration is confirme
 d. \n\nYou will be informed by email of your registration confirmation. Up
 on reception of the confirmation email\, participants will be asked to con
 firm attendance by paying the fees within 5 days.\n\nApplications will clo
 se on *20/05/2026* or as soon as the places will be filled up. Cancellatio
 n after *20/05/2026* will not be reimbursed. Please note that participatio
 n in SIB courses is subject to our [general conditions](https://www.sib.sw
 iss/training/terms-and-conditions).\n\n## Venue and Time\n\nThe course wil
 l will start at 9:00 CEST and end around 17:00 CEST and will take place at
  the [Irchel campus](https://students.uzh.ch/de/dates/sites/irchel.html) o
 f the University of Zurich. More information will follow in due time. \n\n
 Precise information will be provided to the registered participants in due
  time.\n\n\n## Additional information\n\nCoordination: Geert van Geest\n\n
 We will recommend 0.75 ECTS credits for this course (given a passed exam a
 t the end of the course).\n\nYou are welcome to register to the SIB course
 s mailing list to be informed of all future courses and workshops\, as wel
 l as all important deadlines using the form [here](https://lists.sib.swiss
 /mailman/listinfo/courses).\n\nPlease note that participation in SIB cours
 es is subject to our [general conditions](http://www.sib.swiss/training/te
 rms-and-conditions).\n\nSIB abides by the [ELIXIR Code of Conduct](https:/
 /elixir-europe.org/events/code-of-conduct). Participants of SIB courses ar
 e also required to abide by the same code.\n\nFor more information\, pleas
 e contact [training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Introduction to Spatial Transcriptomics Data Analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20260603_ISTDA
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