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DTSTAMP:20260618T090152Z
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DTSTART:20240527T000000Z
DTEND:20240529T000000Z
DESCRIPTION:# Overview\nSingle-cell RNA sequencing (scRNA-seq) can measure 
 the gene expression of complex biological systems at the level of individu
 al cells\, enabling scientists to generate detailed tissue atlases describ
 ing the transcriptomic profiles of thousands or even millions of cells. Wh
 ile scRNA-seq has become a popular technique in diverse fields of biologic
 al research\, the required expertise for handling such datasets has restri
 cted its use among the larger scientific community. The aim of this 3-day 
 course is to empower researchers to start applying the fundamental scRNA-s
 eq analysis pipeline to their own data. We will outline how to design and 
 interpret results of a scRNA-seq dataset and\, in teams\, explore the basi
 cs of preprocessing and analysis in Python on real data. We will discuss c
 ommon concerns in the field\, including preprocessing choices\, dimensiona
 lity reduction\, cell type clustering and identification\, batch effect co
 rrection\, and pseudotime methods. By the end of the course\, participants
  will be able to run CellRanger\, evaluate the quality of a scRNA-seq expe
 riment\, perform scanpy analysis on their own data\, and confidently commu
 nicate about how to overcome potential bottlenecks. The course will be tau
 ght in Python.\n\n# Audience\nThis course is addressed to life scientists 
 and bioinformaticians familiar with some next-generation sequencing approa
 ches and plan to use scRNA-seq in their research projects\, and who are in
 terested in learning how to navigate and analyze such data.  \n\n# Learnin
 g outcomes\nAt the end of the course\, the participants are expected to:\n
 * distinguish advantages and pitfalls of scRNA-seq \n\n* design their own 
 scRNA-seq experiment \n\n* apply a downstream analysis using Python \n\n* 
 interpret and overcome common technical challenges of single-cell analysis
  \n\n# Prerequisites\n**Knowledge**\n* Participants should already have a 
 basic knowledge in Next Generation Sequencing (NGS) techniques\, or have a
 lready followed the "[NGS - Quality control\, Alignment\, Visualisation](h
 ttps://www.sib.swiss/training/course/20240424_NGSQC)".\n* Knowledge in RNA
  sequencing is mandatory.\n* Basic knowledge of Python is required. [Test 
 your Python skills with the quiz here\, before registering](https://forms.
 gle/iCydNS8LUUkm7csz7).\n\n**Technical**\nYou are required to bring your o
 wn laptop. Data and tutorials used in the course will be provided ahead of
  the start date and will be executed using Jupyter notebooks and Anaconda.
  \n\n# Program\nThe Program will be communicated in due time.\n\n\n# Appli
 cation\nThe registration fees for academics are **300 CHF** and **1500 CHF
 ** for for-profit companies.\n\nYou will be informed by email of your regi
 stration confirmation. Upon reception of the confirmation email\, particip
 ants will be asked to confirm attendance by paying the fees within 5 days.
 \n\nDeadline for free-of-charge cancellation is set to *13/05/2024*. Cance
 llation after this date will not be reimbursed. Please note that participa
 tion in SIB courses is subject to our [general conditions](https://www.sib
 .swiss/training/terms-and-conditions).\n\n# Venue and Time\nThis course wi
 ll take place at the University of Bern.\n\nIt will start at 9:15 CET and 
 end around 17:15 CET every day.\n\n\n\nPrecise information will be provide
 d to the participants in due time.\n\n\n#  Additional information\nCoordin
 ation: Valeria Di Cola\, SIB Training Group.\n\nWe will recommend 0.75 ECT
 S 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 to be infor
 med of all future courses and workshops\, as well as all important deadlin
 es using the form [here](https://lists.sib.swiss/mailman/listinfo/courses)
 .\n\nPlease note that participation in SIB courses is subject to our [gene
 ral conditions](https://www.sib.swiss/training/terms-and-conditions).\n\nS
 IB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/events
 /code-of-conduct). Participants of SIB courses are also required to abide 
 by the same code.\n\nFor more information\, please contact [training@sib.s
 wiss](mailto://training@sib.swiss).
SUMMARY:Single-Cell Transcriptomics with Python
URL;VALUE=URI:https://www.sib.swiss/training/course/20240527_SCTPY
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