Path: blob/main/events/tracks/gta2025-single-cell.md
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---layout: event-track title: Single Cell description: Learn all about Single Cell on Galaxy. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel [gta_single-cell](https://gtnsmrgsbord.slack.com/channels/{{page.slack_channel}}). slack_channel: gta_single-cell contributions: organisers: - pavanvidem - nomadscientist instructors: - annasyme - Nilchia - dianichj - hrhotz - igormakunin - jennaj - MarisaJL - pavanvidem - nomadscientist program: - section: "Introduction" description: | Introduction lecture to single-cell data analysis and data formats. tutorials: - name: scrna-intro topic: single-cell - name: scrna-data-formats topic: single-cell - section: "Raw sequencing data to count matrix" description: | Generate a cell-by-gene matrix from droplet-based single-cell RNA sequencing data. tutorials: - name: scrna-preprocessing-tenx topic: single-cell - name: scrna-case_alevin topic: single-cell - section: "Your first analysis based on Scanpy toolkit" description: | This section includes standard single-cell data analysis, including preprocessing, clustering and the identification of cell types via known marker genes; and pseudobulk analysis to help in understanding cell-type-specific gene expression changes. The whole analysis uses Anndata objects, Scanpy toolkit and decoupler. tutorials: - name: scrna-scanpy-pbmc3k topic: single-cell - name: pseudobulk-analysis topic: single-cell - section: "Your first analysis based on Seurat tools" description: | This section includes single-cell data analysis including preprocessing, clustering and the identification of cell types via known marker genes. The whole analysis uses Seurat objects and Seurat R package. tutorials: - name: scrna-seurat-pbmc3k topic: single-cell
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