hands-on tutorial
Hands-on for 'Clustering 3K PBMCs with Scanpy' tutorial
The questions this addresses are:
- What are the steps to prepare single-cell RNA-Seq data for clustering?
- How to cluster cells in single-cell RNA-Seq data?
- How cell type annotation can be assigned to cell clusters?
The objectives are:
- Describe an AnnData object to store single-cell data
- Explain the preprocessing steps for single-cell data
- Evaluate quality of single-cell data and apply steps to select and filter cells and genes based on QC
- Execute data normalization and scaling
- Identify highly variable genes
- Construct and run a dimensionality reduction using Principal Component Analysis
- Perform a graph-based clustering for cells
- Identify marker genes for the clusters
- Construct and run a cell type annotation for the clusters
Licence: Creative Commons Attribution 4.0 International
Keywords: single-cell, single-cell, 10x
Target audience: Students
Resource type: hands-on tutorial
Contributors: Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman
Scientific topics: Transcriptomics
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