Single Cell
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.
Pavankumar Videm
Wendi Bacon
Anna Syme
Amirhossein Naghsh Nilchi
Diana Chiang Jurado
Hans-Rudolf Hotz
Igor Makunin
Jennifer Hillman-Jackson
Marisa LoachNeed help with these tutorials?
Open Slack support channel for this track: comment #gta_single-cellIntroduction
Introduction lecture to single-cell data analysis and data formats.
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An introduction to scRNA-seq data analysis
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Single-cell Formats and Resources
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Raw sequencing data to count matrix
Generate a cell-by-gene matrix from droplet-based single-cell RNA sequencing data.
| Lesson | Slides | Hands-on | Recordings |
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| Pre-processing of 10X Single-Cell RNA Datasets | |||
| Generating a single cell matrix using Alevin |
Your first analysis based on Scanpy toolkit
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.
| Lesson | Slides | Hands-on | Recordings |
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| Clustering 3K PBMCs with Scanpy | |||
| Pseudobulk Analysis with Decoupler and EdgeR |
Your first analysis based on Seurat tools
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.
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| Clustering 3K PBMCs with Seurat |