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SUMMARY:Course on scRNA-seq Data Analysis
UID:https://www.elixir-czech.cz/events/course-on-scrna-seq-data-analysis-2025
LOCATION:
DTSTAMP:20251201T090000
DTSTART;TZID=Europe/Prague:20251201T090000
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DESCRIPTION:AboutSingle-cell RNA sequencing (scRNA-seq) allows researchers to study
gene expression at the level of individual cells. This approach can, for
example, help to identify different cell populations in a complex sample
and describe their expression patterns. To generate and analyse scRNA-seq
data, several methods are available, all with their strengths and
weaknesses depending on the researchers’ needs. This 3-day course will
cover the main technologies as well as the main aspects to consider while
designing an scRNA-seq experiment. In particular, it will combine the
theoretical background of analytical methods with hands-on data analysis
sessions focused on data generated by droplet-based platforms.By the end of
the course, participants will possess the following abilities:Distinguish
advantages and pitfalls of scRNA-seq.Design their own scRNA-seq experiment,
using common technologies like 10× Genomics.Apply quality control (QC)
measures and utilise analysis tools to preprocess scRNA-seq data.Apply
normalisation, scaling, dimensionality reduction, integration and
clustering on scRNA-seq data using R.Differentiate between cell annotation
techniques to identify and characterise cell populations.Use differential
gene expression analysis methods on scRNA-seq data to gain biological
insights.Select enrichment analysis methods appropriate to the biological
question and data.Develop an scRNA-seq data analysis workflow from raw
count matrix to differential gene expression with peer support and light
guidance. Dates: 1.-3.12.2025Location: Institute of Molecular Genetics of
the Czech Academy of Sciences, Vídeňská 1083 Praha 4, Jágr’s
hallMaximum capacity: 25 participantsProgrammeDay 1 – Monday December
1st       9:00 -    9:30  Introduction       9:30 - 10:30 
Introduction to scRNA-seq    10:30 - 11:00  Break    11:00 - 12:30 
10× and Cellranger    12:30 - 13:30  Lunch    13:30 - 15:00 
Analysis tools and QC    15:00 - 15:30  Break    15:30 - 17:00  Group
work Day 2 – Tuesday December 2nd       9:00 - 10:30  Normalisation
and scaling    10:30 - 11:00  Break    11:00 - 12:30  Dimensionality
reduction and integration    12:30 - 13:30  Lunch    13:30 - 15:00 
Clustering    15:00 - 15:30  Break    15:30 - 17:00  Group work Day
3 – Wednesday December 3rd       9:00 - 10:30  Cell annotation   
10:30 - 11:00  Break    11:00 - 12:30  Differential gene expression 
  12:30 - 13:30  Lunch    13:30 - 15:00  Group work    15:00 -
15:30  Break    15:30 - 17:00  Group work +
presentations InstructorsLucie Pfeiferová (IMG)Jan Kubovčiak (IMG)Yusuf
Çağlar Odabaşı (IBT)Mathys Delattre (IMG)Michal Kolář (IMG)Vojtěch
Melichar (IMG) RequirementsThis course is designed for life scientists and
bioinformaticians with experience in next-generation sequencing who aspire
to analyse scRNA-seq gene expression data. The course exercises are
conducted in the R statistical language, so a basic understanding of R and
RStudio is essential and strictly required. Participants are encouraged to
bring their own laptops with a modern internet browser to access the remote
computational environment, which will be used during the course; however,
workstations will be provided upon request. For any queries on software
requirements, please reach out to lucie.pfeiferova@img.cas.cz,
jan.kubovciak@img.cas.cz, or michal.kolar@img.cas.cz. AttributionThis
course is heavily based on the course developed by the Swiss Institute of
Bioinformatics (https://sib-swiss.github.io/single-cell-r-training/). It
also draws inspiration from the Broad Institute Single Cell Workshop and
the CRUK CI Introduction to Single-Cell RNA-Seq Data Analysis
course. RegistrationThe course is provided by ELIXIR-Czech, no participant
fee is collected. Applications are closed as the course is full. Feedback
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