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DTSTAMP:20260616T091703Z
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DTSTART:20251209T090000Z
DTEND:20251210T170000Z
DESCRIPTION:# Introduction to Sequencing-based Spatial Transcriptomics Data
  Analysis\n\n## Overview\n\nSpatial transcriptomics is a rapidly evolving 
 technology that allows researchers to study gene expression within the spa
 tial context of tissue architecture. This course provides a practical intr
 oduction to the analysis of sequencing-based spatially resolved transcript
 omics (SRT) data\, combining theoretical background with hands-on exercise
 s using mostly the R/[Bioconductor](https://www.bioconductor.org/) ecosyst
 em. Participants will gain an understanding of experimental design\, data 
 preprocessing\, and downstream analysis workflows. Through lectures and gu
 ided practicals\, the course aims to equip participants with the skills ne
 eded to perform their own spatial transcriptomics analyses and interpret t
 he results in a biological context.\n\n\n## Audience\n\nThis course is aim
 ed at PhD students\, postdoctoral and other researchers in the life scienc
 es who are seeking to understand and analyze spatial transcriptomics data.
 \n\n## Learning outcomes\n\nAt the end of the course\, the participants ar
 e expected to:\n\n- Explain the principles and describe applications of se
 quencing-based spatially-resolved transcriptomics (SRT)\n- Define the diff
 erences between sequencing-based SRT methods and imaging-based SRT methods
 .\n- Identify potential pitfalls and limitations of sequencing-based SRT e
 xperiments and analysis workflows.\n- Assess and interpret raw sequencing 
 outputs and spatial metadata files\, understanding their structure and rel
 evance for downstream analyses.\n- Define important aspects of quality con
 trol\, feature selection\, dimensionality reduction and differentail gene 
 expression to SRT data and apply those. \n- Clarify various spatial statis
 tics and their application to biological questions.\n- Use frequently-used
  methods to analyze multi-sample SRT experiments.\n\n\n## Prerequisites\n\
 n### Knowledge\nYou should meet the learning outcomes of: \n\n- [Introduct
 ion to bulk RNA-Seq: From Quality Control to Pathway Analysis](https://www
 .sib.swiss/training/course/20250922_IRNAS)\n- [Introduction to Sequencing 
 Data Analysis](https://www.sib.swiss/training/course/20251119_ISEDA)\n- [F
 irst Steps with R in Life Sciences](https://www.sib.swiss/training/course/
 20251013_FSWR)\n- [Single-Cell Transcriptomics with R](https://www.sib.swi
 ss/training/course/20241112_ISCTR)\n\nIn summary\, participants must alrea
 dy have a basic knowledge in:\n- Next Generation Sequencing (NGS) techniqu
 es\n- Analyzing gene expression data\n- Dimensionality reduction (PCA\, UM
 AP)\n- Graph-based clustering \n- `R` (evaluate your `R` skills [here](htt
 ps://docs.google.com/forms/d/e/1FAIpQLSdIyeuabd_ZOWXgI1MWHapmaOMu20L9ESkLD
 ZiWnpmkpujyOg/viewform?usp=sf_link))\n- `UNIX` (self-assess your skills wi
 th the e-learning course [`UNIX` Fundamentals](https://www.sib.swiss/train
 ing/course/2012_UNIXF)\, and this [quiz](https://docs.google.com/forms/d/e
 /1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_
 link))\n\n### Technical\n\nAttendees should have a Wi-Fi enabled computer.
  An online R and RStudio environment will be provided. However\, in case y
 ou wish to perform the practical exercises on your own computer\, please t
 ake a moment to install R (&gt\; 4.5) and Rstudio before the course.\n\n##
  Application\n\nThe registration fees for academics are **CHF 200** and **
 CHF 1000** for for-profit companies. While participants are registered on 
 a first come\, first served basis\, exceptions may be made to ensure diver
 sity and equity\, which may increase the time before your registration is 
 confirmed. \n\nYou will be informed by email of your registration confirma
 tion. Upon reception of the confirmation email\, participants will be aske
 d to confirm attendance by paying the fees within 5 days.\n\nApplications 
 close on **02/12/2025** or as soon as the places will be filled up. Deadli
 ne for free-of-charge cancellation is set to **02/12/2025**. Cancellation 
 after this date will not be reimbursed. Please note that participation in 
 SIB courses is subject to our [general conditions](https://www.sib.swiss/t
 raining/terms-and-conditions).\n\n## Venue and Time\n\nThe course will tak
 e at Bern University. \n\nThe course will start at 9:15 and end around 17:
 00. \n\nPrecise information will be provided to the participants in due ti
 me.\n\n\n## Additional information\n\nCoordination: Geert van Geest\n\nWe 
 will recommend 0.5 ECTS credits for this course (given a passed exam at th
 e end of the course).\n\nYou are welcome to register to the SIB courses ma
 iling list to be informed of all future courses and workshops\, as well as
  all important deadlines using the form [here](https://lists.sib.swiss/pos
 torius/lists/courses.lists.sib.swiss/).\n\nPlease note that participation 
 in SIB courses is subject to our [general conditions](https://www.sib.swis
 s/training/terms-and-conditions).\n\nSIB abides by the [ELIXIR Code of Con
 duct](https://elixir-europe.org/events/code-of-conduct). Participants of S
 IB courses are also required to abide by the same code.\n\nFor more inform
 ation\, please contact [training@sib.swiss](mailto:training@sib.swiss).
SUMMARY:Introduction to Sequencing-based Spatial Transcriptomics Data Analy
 sis
URL;VALUE=URI:https://www.sib.swiss/training/course/20251209_SBSRT
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