{"id":809,"name":"Introduction to single-cell RNAseq analysis","shortName":"Introduction to single-cell RNAseq analysis","description":"Objectives\r\n- Understand and learn the main steps of scRNA-seq data analysis, up to marker gene detection and cell type identification.\r\n- Be able to use the Seurat package on a small test dataset, from count matrices to clustering and cluster annotation.\r\n- Understand the basics of the analysis in order to apply them to one’s own dataset.\r\n\r\nCourse Content\r\nI. Introduction\r\n- Single-cell RNA sequencing\r\n- From raw sequencing data to count matrices\r\n- Software tools\r\n\r\nII. Preprocessing of the expression matrix (Theory and Practice)\r\n- Quality control\r\n- Normalization\r\n- Dimensionality reduction (HVG, PCA, UMAP)\r\n- Detection of expression biases\r\n\r\nIII. Annotation (Theory and Practice)\r\n- Clustering\r\n- Marker genes\r\n- Cell type identification\r\n- Analysis of marker gene lists with the R package ClusterProfiler\r\n\r\nIV. Practical Workshop “Bring your own data”\r\n- Semi-autonomous execution of primary analysis on learners’ own data","homepage":"https://pf-bird.univ-nantes.fr/training/singlecell/","is_draft":false,"costs":["Priced"],"topics":[],"keywords":[],"prerequisites":[],"openTo":"Everyone","accessConditions":"1. Good knowledge of R or having completed the training “Bioanalysis Training: Introduction to the R Programming Language.”\r\n\r\n2. Have your own data or data of interest collected from public databases (cellXgene, Single Cell Portal, …).","maxParticipants":20,"contacts":[],"elixirPlatforms":[],"communities":[],"sponsoredBy":[],"organisedByOrganisations":[],"organisedByTeams":[{"id":16,"name":"BiRD","url":"https://catalogue.france-bioinformatique.fr/api/team/BiRD/?format=json"}],"logo_url":"https://bird.univ-nantes.io/website/images/logo/logo.svg","updated_at":"2026-09-03T15:09:40.096491Z","type":"Training course","start_date":"2026-10-19","end_date":"2026-10-21","venue":"","city":"Nantes","country":"","geographical_range":"","trainers":[],"trainingMaterials":[],"computingFacilities":[],"realisation_status":"future","registration_opening":"2026-09-01","registration_closing":"2026-10-02","registration_status":"open","courseMode":"Onsite"}