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Pseudo-Bulk Analysis for Single-Cell RNA-Seq Data - Detailed Workflow Tutorial
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- 1 Intro
- 2 WHAT is pseudo-bulk analysis?
- 3 WHY perform pseudo-bulk analysis?
- 4 onwards HOW to perform pseudo-bulk analysis?
- 5 Fetch data from ExperimentHub
- 6 QC and filtering
- 7 Seurat's standard workflow steps
- 8 Visualize data
- 9 To use integrated or nonintegrated data?
- 10 Aggregate counts to sample level
- 11 Data manipulation step 1: Transpose matrix
- 12 Data manipulation step 2: Split data frame
- 13 Data manipulation step 3: Fix row.names and transpose again
- 14 DESeq2 step 1: Get count matrix corresponding to a cell type
- 15 : Create sample level metadata i.e. colData
- 16 DESeq2 step 2: Create DESeq2 dataset from matrix
- 17 DESeq2 step 2: Run DESeq
- 18 Get results
