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DTSTART:20251112T090000Z
DTEND:20251114T170000Z
DESCRIPTION:# Overview\n\nSingle-cell RNA sequencing (scRNAseq) allows rese
 archers to study gene expression at the single cell level. For example\, s
 cRNAseq can help to identify expression patterns that differ between condi
 tions within a cell-type. To generate and analyze scRNAseq data\, several 
 methods are available\, all with their strengths and weaknesses depending 
 on the researchers’ needs. This 3-day course will cover the main technol
 ogies as well as the main aspects to consider while designing a scRNAseq e
 xperiment. In addition\, it will cover the theoretical background of analy
 sis methods with hands-on practical data analysis sessions applied to drop
 let-based methods.\n\n# Audience\n\nThis course is intended for life scien
 tists and bioinformaticians familiar with "Next Generation Sequencing" who
  want to acquire the necessary skills to analyse scRNA-seq gene expression
  data.\n\n# Learning objectives\n\nAt the end of the course\, participants
  will be able to:\n\n* Distinguish advantages and pitfalls of scRNA-seq\, 
 including its applications in experimental design.\n* Design their own scR
 NA-seq experiment\, by using common technologies like 10X Genomics.\n* App
 ly quality control (QC) measures and utilize analysis tools to preprocess 
 scRNA-seq data.\n* Apply normalization\, scaling\, dimensionality reductio
 n\, and integration and clustering on single-cell transcriptomics data tec
 hniques using R.\n* Differentiate between cell annotation techniques to id
 entify and characterize cell populations.\n* Use differential gene express
 ion analysis methods on single-cell transcriptomics data to gain biologica
 l insights.\n* Select enrichment analysis methods appropriate to the biolo
 gical question and data.\n* Develop a single-cell transcriptomics data ana
 lysis workflow from raw count matrix to differential gene expression with 
 peer support and light guidance.\n\n# Prerequisites\n\n*Knowledge*\n\n\n\n
 You should meet the learning outcomes of:\n[**Introduction to bulk RNA-Seq
 : From Quality Control to Pathway Analysis**](https://www.sib.swiss/traini
 ng/course/20250922_IRNAS).\n\nYou should also meet the learning outcomes o
 f: [**NGS - Quality control\, Alignment\, Visualisation**](https://www.sib
 .swiss/training/course/20250423_NGSQC) and [**First Steps with R in Life S
 ciences**](https://www.sib.swiss/training/course/20251013_FSWR).\n\nIn sum
 mary\, participants must already have a basic knowledge in **Next Generati
 on Sequencing (NGS) techniques**\, **R** (evaluate your R skills [here](ht
 tps://docs.google.com/forms/d/e/1FAIpQLSdIyeuabd_ZOWXgI1MWHapmaOMu20L9ESkL
 DZiWnpmkpujyOg/viewform?usp=sf_link)) and **UNIX** (self-assess your skill
 s with the e-learning course [UNIX Fundamentals](https://www.sib.swiss/tra
 ining/course/2012_UNIXF)\, and this [quiz](https://docs.google.com/forms/d
 /e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=s
 f_link)).\n\n*Technical*\n\nAttendees should have a Wi-Fi enabled computer
 . **An online R and RStudio environment will be provided.** However\, in c
 ase you wish to perform the practical exercises on your own computer\, ple
 ase take a moment to install the following before the course:\n*  R versio
 n &gt\; 4.2.\n*  Latest RStudio version\, the free version is perfectly fi
 ne.\n\n\n\n# Program\n\nThe program will be communicated in due time. Prog
 ram of past occurences can be found on [GitHub](https://sib-swiss.github.i
 o/single-cell-training/course_schedule.html).\n\n\n\n# Application\n\n\n\n
 \n\nThe registration fees for academics are **300 CHF** and **1500 CHF** f
 or for-profit companies. While participants are registered on a first come
 \, first served basis\, exceptions may be made to ensure diversity and equ
 ity\, which may increase the time before your registration is confirmed.\n
 \nApplications will close once the places will be filled\, untll **05/11/2
 025**. Deadline for free-of-charge cancellation is set to **29/10/2025**. 
 Cancellation after this date will not be reimbursed. Please note that part
 icipation in SIB courses is subject to our [general conditions](https://ww
 w.sib.swiss/training/terms-and-conditions).\n\nYou will be informed by ema
 il of your registration confirmation. Upon reception of the confirmation e
 mail\, participants will be asked to confirm attendance by paying the fees
  within 5 days.\n\n# Venue and Time\n\n\n\nThe course will ONLY take place
 \, in person\, at the Bellinzona Institutes of Science (BIOS+) building\, 
 Via Francesco Chiesa 5\, Bellinzona\, Ticino.\n\n\n\nIt will start at 9:00
  CET and end around 17:00 CET every day.\n\n\nPrecise information will be 
 provided to the participants in due time.\n\n\n# Additional information\n\
 nCoordination: Grégoire Rossier\, SIB Training group.\n\nWe will recommen
 d 0.75 ECTS credits for this course (given a passed exam at the end of the
  course).\n\nYou are welcome to register to the SIB courses mailing list t
 o be informed of all future courses and workshops\, as well as all importa
 nt deadlines using the form [here](https://lists.sib.swiss/postorius/lists
 /courses.lists.sib.swiss/).\n\nPlease note that participation in SIB cours
 es is subject to our [general conditions](https://www.sib.swiss/training/t
 erms-and-conditions).\n\nSIB abides by the [ELIXIR Code of Conduct](https:
 //elixir-europe.org/events/code-of-conduct). Participants of SIB courses a
 re also required to abide by the same code.\n\nFor more information\, plea
 se contact [training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Single-Cell Transcriptomics with R
URL;VALUE=URI:https://www.sib.swiss/training/course/20241112_ISCTR
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