4th Workshop Single-Cell / SincellTE 2022 / Single-Cell : Transcriptomics, Spatial and Multi-Omics

Topic outline

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  General

  • Annonces Forum
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    Duration

    This fourth edition of the school will be held from 09 January 2022 to 14th january 2022 at the Roscoff Biological Station (France).

    Objectives

    This workshop focuses on the large-scale study of heterogeneity across individual cells from a genomic, transcriptomic and epigenomic point of view. New technological developments enable the characterization of molecular information at a single cell resolution for large numbers of cells. The high dimensional omics data that these technologies produce raise novel methodological challenges for the analysis. In this regard, dedicated bioinformatics and statistical methods have been developed in order to extract robust information.

    The workshop aims to provide such methods for engineers and researchers directly involved in functional genomics projects making use of single-cell technologies. A wide range of single cell topics will be covered in lectures, demonstrations and practical classes. Among others, the areas and issues to be addressed will include the choice of the most appropriate single-cell sequencing technology, the experimental design and the bioinformatics and statistical methods and pipelines. For this edition, new courses/practicals will focus on spatial transcriptomics, cell phenotyping and additional multi-omics.

    Participants

    This course is directed towards 30 engineers and researchers who regularly need to undertake single-cell data analysis as well as PhD candidates and Postdocs in computational biology or bioinformatics that are interested in the development of methods and pipelines for high dimension single-cell data analysis.

    Working environment

    Unix command will be used for bioinformatic analysis, and R programming language for statistical analysis.

    Prerequisites

    Participants must have prior experience on NGS data analysis  with everyday use of R and good knowledge of Unix command line. Before the training, participants will be asked to familiarize themselves with the processing and primary analyses steps of scRNA-seq datasets with provided pedagogic material. Study material : Already working on his/her own single cell dataset is not mandatory.

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  Organisation of the week

  • UPDATED Planning sincellTE 2022 File
  • welcome File
  • Scientific coordination:
    

    • Marie-Agnès Dillies (Institut Pasteur Paris),
      
    • Morgane Thomas-Chollier (IBENS CNRS UMR8197, ENS, INSERM U1024),
      
    • Agnès Paquet (Syneos Health, Sophia-Antipolis),
      
    • Nicolas Servant (Institut Curie, INSERM U900, Mines ParisTech),
      
    • Marc Deloger (Gustave Roussy),
      
    • Kevin Lebrigand (UCAGenomiX IPMC CNRS),
      
    • Erwan Corre (ABIMS FR2424 CNRS-UPMC, Station Biologique de Roscoff)
      
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  Technologies, experimental approaches, primary analysis

  • Kevin Lebrigand - Technologies & experimental approaches - part 1 File
  • Kevin Lebrigand - Technologies & experimental approaches - part 2 File
  • Rémi Montagne - Marine Aglave - Mapping-Quality-Check-Quantification File
  • Agnès Paquet - Experimental Design Normalization File
  • Hands-on session
    

  • Practical : Primary Analyses File
  • Primary analysis Markdown File
  • Primary analysis MarkDown (HTML without) File
  • Primary analysis MarkDown (HTML with) File
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  Statistical models and secondary analyses

  • Akira Cortal - Statistical models and analyses File
  • Hands-on session
    

  • Practical : Statistical models and analyses File
  • Statistical models and analyses MarkDown (HTML) File
  • Statistical models and analyses MarkDown File
  • Agnès Paquet - Nicolas Nottet - Secondary Analysis File
  • Hands-on session
    

  • Practical Cell Type Annotation File
  • TP Cell annotation (HTML) File
  • TP Cell annotation (MarkDown) File
  • TP Secondary Analyses scGSVA (HTML) File
  • TP Secondary Analyses Trajectory (HTML) File
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  Spatial transcriptomics

  • Bastien Job - Visium File
  • Mario Acera - Data Modalitites Unsupervised Analisis File
  • Marc Eluosa - Advance Spatial Analysis File
  • Kevin Lebrigand - Spatial isoform transcriptomics File
  • Hands-on session
    

  • spatial analysis (MarkDown) File
  • Spatial Analysis (GitHub) URL
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  Epigenomics and multi-omics

  • Andres Quintero - Epigenomics File
  • Andres Quintero - Multi-Omics File
  • Hands-on session
    

  • Andres Quintero - Practical URL
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  RNA Velocity and ISee

  • Agnes Paquet - RNA Velocity Course Set-Up File
  • Charlotte Soneson - website URL