Workshop CNRS Single-Cell 2020
Ecole thématique CNRS Single-Cell // Transcriptomique et épigénomique en cellule unique: théorie et pratique (sincellTE)
Du 27-09-2020 au 02-10-2020 à Station Biologique Roscoff
Date limite d'inscription: 15-01-2020



This third edition of the school will be held from 27 september to 02 October 2020 at the Roscoff Biological Station (France).


This school focuses on the study of heterogeneous cell populations from the genomic, transcriptomic and epigenomic point of view. Technologies enable the characterization of molecular information at a single cell resolution for large numbers of cells evolve rapidly and lead to the generation of new types of data associated with new methodological issues. In order to follow these technological evolutions, dedicated bioinformatic and biostatistical methods are developed allowing to take into account the specificity of these data and to propose adapted methods of analysis.

The school aims to explain and disseminate these methods within the community of engineers and researchers, bioinformaticians and statisticians directly involved in single-cell functional genomics projects. This course offers a complete formation including the choice of the best adapted technology to the biological question posed, the design of the experiment, the quality control and, in particular, the associated bioinformatic and statistical analyzes. The school will be based on an alternation of theoretical sessions and practical workshops.


This training is intended for about 30 engineers and research executives involved in the regular analysis of single-cell data, as well as doctoral and post-doctoral students in computational biology and bioinformatics interested in the development and application of research methodologies. high-dimensional single-cell analysis.

Working environment

The entire training will be based on the use of online commands (Linux terminal) for bioinformatic analysis, and the R language for statistical analysis.


Knowledge of tools and pipelines to analyze high-throughput sequencing data (RNA-seq or Hi-C or ATAC-seq bulk). Participants must already practice high throughput sequencing data analysis, with daily use of the R language, the Rstudio environment and a good knowledge of the Unix command line. You do not have to have a single-cell data analysis project.

Registration details

Deadline for pre-registration: January 15, 2020 (selection of participants: February 1, 2020). 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 for academic staff

600 € HT = 720 € TTC (cost already covered for staff paid by the CNRS);

for the industrialists: 1.750 € HT = 2.100 € TTC. Accommodation and catering are included.

Scientific coordination: Marie-Agnès Dillies, C3BI (USR 3756 IP CNRS), Morgane Thomas-Chollier, IBENS (CNRS UMR8197, ENS, INSERM U1024), Agnès Paquet, SYNEOS Health (Sophia-Antipolis), Antonio Rausell (Imagine Institute , INSERM UMR-1163), Nicolas Servant (Institut Curie, INSERM U900, Mines ParisTech), Marc Deloger (Gustave Roussy)

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

Administrative management​​ :​ ​ Département de Biologie Computationnelle 



click on the image to obtain a PDF version

The slides are deposited on this page during the course :

Follow the course on Twitter #sincellTE

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.

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.

- breakfast will be organized in two successive “sessions” to allow physical distancing

- in the hotel, a flow direction will be set up to avoid people to cross each other

- lunches and dinners will take place in a large room with space between tables and people (max 4 persons per table)

- we will provide masks for participants. Wearing a mask will be mandatory during classes and in the station.

- we will provide hydroalcoholic gel to participants : Hydroalcoholic gel will be available at the entrance of the classroom, during the coffee breaks, at the entrance of the hotel.

- coffee breaks will take place in the breakfast room of the Hotel de France to allow physical distancing during the breaks. If the weather allows it, the breaks will be taken outside.

- we will ask participants to keep the same spot in the classroom during the entire week. Cleaning lotion will be available to participants for their table.

- windows of the classroom will be open during the breaks and even during classes if possible (according to the weather).

- two lectures will be provided online. We ask you to bring your own headphones to attend these classes.

Of course we will ask everyone to respect barrier gestures and official recommendations in order to keep the school as safe as possible. Please feel free to contact us if you have questions or suggestions about this protocol.

Marie-Agnès Dillies (C3BI USR 3756 IP CNRS)

Dr Marie-Agnès Dillies is co-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, in the team Computational Systems Biology at IBENS. She has expertise in epigenomics (ChIP-seq, ChIP-exo) and motif analysis in genomic sequences, and single-cell transcriptomics. 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. She used to be the head of biostatistics for the Functional Genomics Plateforme of the Institut de Pharmacologie Moleculaire et Cellulaire (Sophia Antipolis, France), before joining SYNEOS Health.

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 type of NGS data but mainly in RNA-seq, WES and ChIP-seq. 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.

Antonio Rausell (Institut Imagine, INSERM UMR-1163)

Dr. Antonio Rausell is the Director of the Clinical Bioinformatics Lab of the Institut Imagine. He has an expertise in bioinformatics and high-dimensional single-cell data analysis.


Luca Albergante (Sensyne Health, UK)

Akira Cortal (Institut Imagine, INSERM UMR-1163)

Kevin Lebrigand (UCAGenomiX IPMC CNRS)

Nathalie Lehmann (IBENS CNRS UMR8197, ENS, INSERM U1024)

Bastien Job (Gustave Roussy)

Christophe Becavin (Research Assistant Professor at Université Côte d'Azur)

Christophe Fleury (10X Genomics)

Laura Cantini (IBENS CNRS UMR8197, ENS, INSERM U1024)

Claire Lansonneur ((IBENS CNRS UMR8197, ENS, INSERM U1024)

Q. Le matériel (slides, etc) sera-t-il disponible en ligne après l'évènement pour celles et ceux qui ne peuvent pas participer ?

R. 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 le site web, dans la section "course material".

Q. Comment savoir si je peux bénéficier du tarif "académique" ou pas ?

R. 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.

Q. Est-il possible d'effectuer plusieurs candidatures par laboratoire ?

R. 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.

Q. La formation est-elle en anglais ou en français ?

R. La formation sera dispensée en anglais