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

Practical informations

  Fichier:Centre national de la recherche scientifique.svg — WikipédiaINCEPTION- Call for Interdisciplinary Research Projects (P2I call) -  Research - Institut PasteurLogo France Génomique

The workshop obtained the label Ecole thématique du CNRS 2022



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


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.


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.


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.

Registration details

Deadline for pre-registration: September 15, 2021 (selection of participants: October 20, 2021). The number of places being limited (30 participants), the organizing committee will select the participants according to the information given during this pre-registration.

Registration fees

The registration fee includes accommodation and meals.

academic/university : 650 € HT = 780 € TTC  (fee covered for CNRS personnel if the workshop is sponsored by CNRS. Information available mid-december 2021);

private sector: 1.750 € HT = 2.100 € TTC.

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)

Technical coordination: Erwan Corre (ABIMS FR2424 CNRS-UPMC, Station Biologique de Roscoff)

Administrative management​​ :​ ​ Département de Biologie Computationnelle  


Marie-Agnès Dillies (Institut Pasteur) Dr Marie-Agnès Dillies is head of the Bioinformatics and Biostatistics Hub of the Institut Pasteur. She has expertise in statistical analysis of gene expression data (Dillies et al, Briefings in Bioinformatics 2013). She is co-animating the StatOmique group. Recently she joined the Pasteur Single Cell Initiative.

Morgane Thomas-Chollier (IBENS CNRS UMR8197, ENS, INSERM U1024) Dr. Morgane Thomas-Chollier is Associate Professor in Bioinformatics at Ecole Normale Supérieure Paris and co-head of the ENS Genomics platform. She has expertise in single-cell transcriptomics, bulk epigenomics (ChIP-seq, ChIP-exo) and motif analysis in genomic sequences. She was heading the French Society for Bioinformatics (SFBI) until recently.

Agnès Paquet (SYNEOS Health, Sophia Antipolis) Agnes Paquet is an expert in statistical analysis and mining of large datasets from high-throughput assays (microarrays, NGS data such as RNAseq and single cell RNAseq). She is specialized in biomarkers discovery and in development of assays for diagnostic and resistance assessment in HIV, HCV, breast and lung cancers.

Marc Deloger (Gustave Roussy) Dr Marc Deloger is Head of Bioinformatics Core Facility of Gustave Roussy Hospital. He has expertise in analysis of many different types of NGS data but mainly in RNA-seq (bulk, single-cell and long reads) and WES. He is part of the BioInformatics French Society (SFBI) council.

Nicolas Servant (Institut Curie, INSERM U900, Mines ParisTech) Dr Nicolas Servant is co-Director of Bioinformatics core facility at Institut Curie, Paris. He has a wide expertise in NGS, including epigenomics, in particular 3D conformation of the chromatin. He recently joined the Institut Curie single-cell initiative.

Kevin Lebrigand (UCAGenomiX IPMC CNRS) Dr Kevin Lebrigand is head of bioinformatics of the UCAGenomiX genomics platform (IPMC, CNRS, Sophia-Antipolis). He is a sinngle cell genomics expert in the "France Genomique" network gathering the main french functional genomics platforms.

Erwan Corre (CNRS - Station Biologique de Roscoff) Dr Erwan Corre is Head of Bioinformatics Core Facility of Roscoff Marine Station (ABiMS - NNCR IFB Platform) providing the computing infrastructure for the training. As a bio‐analyst,  he has expertise in: assembly, curation and annotation of (meta-) transcriptomics and (meta-) genomic sequences on non-model organisms and environmental samples. He is part of the BioInformatics French Society (SFBI) council.



Marine Aglave (Bioinformatics Core Facility, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France)

Dr. Akira Cortal ( PairXBio- Singapore)

Marc Elosua (CNAG - Barcelona, Spain)

Dr. Georges Emanuel (Vizgen)

Dr. Christophe Fleury (10X Genomics)

Bastien Job (Bioinformatics Core Facility, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France)

Mario Acera (Josep Carreras Institute, - Barcelona, Spain)

Dr. Rémi Montagne (Institut Curie Bioinformatics core facility, INSERM U900, Mines Paris Tech -Paris, France)

Paula Nieto (CNAG - Barcelona, Spain)

Nicolas Nottet (Syneos Health Translational Sciences - Biot France)

Dr. Charlotte Soneson (FMI - Basel, Swizerland)

Dr. Andres Quintero (BioQuant-Zentrum - Heidelberg - Germany)

Travel & accommodation
The registration fees includes accomodation and meals. We take care of the reservation of the hotel.

The organization of your trip and the payment of your transport costs are at your expense.

By train: TGV Paris Montparnasse and Morlaix (duration 3 hours) then bus from Morlaix to Roscoff (duration 32 minutes)
By plane: flights from Roissy and Orly to Brest, then taxi from Brest to Roscoff.

If you can share the taxi with others, the price is interesting. We can provide you with detailed information on taxi companies with collaboration from the center of Roscoff. A shared document will be put in place to allow participants wishing to get in touch with people traveling on the same train / plane.
Sanitary precautions
We are preparing the school and we are doing our best together with the Station Biologique to make sure that the school will be held in the best conditions.
To keep the school safe we will all have to follow the rules below (both participants and trainers):
- Wear a mask in all circumstances. Masks will be provided to all participants.
-Follow the direction of movement in buildings and respect the 1m distanciation Hydroalcoolic solution will be available in the buildings and in the classroom.
-Physical distancing will be respected in the classroom. Keep the same seat in the room during the whole week
-The use of elevators is restricted to disabled people
-A valid sanitary pass (or European Union digital Covid certificate) (=valid QR code) will be checked every morning upon arrival in the classroom, by one of the three organisers who have officially received habilitation to check.
-In the current context, we further recommend all attendees and trainers to Wear a FFP2/KN95/KF94 mask in the transportation (train/plane) coming to the school Favor working for home this week to limit contacts Just before travelling to the school, do an autotest.
- In case of doubt during the week, autotests will be available, in addition to a closeby pharmacy performing antigenic tests
Le matériel (slides, etc) sera-t-il disponible en ligne après l'évènement pour celles et ceux qui ne peuvent pas participer ?
Généralement pour ce genre d'école nous demandons aux intervenants de faire une version publiable sur le site web (c'est à dire avec toutes les sources clairement indiquées, en retirant les résultats confidentiels ou non encore publiés etc...). Les documents sont déposés au fur et à mesure sur la plateforme Moodle de l'IFB.
Comment savoir si je peux bénéficier du tarif "académique" ou pas ?
Tout dépend de votre "employeur" officiel et non du laboratoire/institut auquel vous êtes rattaché. Le tarif académique s'applique aux personnels financés par établissement public c'est à dire ayant une fiche de paye provenant d'un EPST (CNRS, IFSTTAR, INED, INRA, INRIA, INSERM, IRD, IRSTEA) ou d'une Université. De plus cette école étant une école CNRS, cela est gratuit pour les agents CNRS.
Est-il possible d'effectuer plusieurs candidatures par laboratoire ?
Il faut "prioritiser" en interne vos candidatures car vue la demande attendue, le nombre de places restreint et la volonté de diffusion la plus large possible au niveau national, il y a quasiment aucune chance que 2 candidatures d'un même laboratoire soient sélectionnées.
La formation est-elle en anglais ou en français ?
La formation sera dispensée en anglais

Archives des versions précédentes de l'école Single Cell

  • Soon online
Les demandes d'inscription sont ouvertes jusqu'au 15/09/2021.
From 09/01/2022 6:00 pm to 14/01/2022 2:00 pm at la Station biologique de Roscoff (France)
Registration deadline: 15/09/2021 12:00 pm
Plaquette FR
Course material
IFB - Institut Français de Bioinformatique ♦ CNRS UAR 3601 ♦ IFB-Core, Génoscope - 2 rue Gaston Crémieux, 91057 - ÉVRY – CEDEX ANR-11-INBS-0013236
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