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📎 Red: Unsolved
Orange: Being Processed
Green: Solved
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Objectives of the Experiment
- To create two simulated cell expression matrices with known cell type proportions
- To apply methods found in the literature to find the signature gene markers of the cell types in the simulated cell expression matrix
- To apply methods found in the literature to determine with statements of statistical significance the proportions of cells in respective cell matrices
Procedures
1. Generation of Cell Expression Matrices
- Summary of the Experiment (Diagram)
1. Generation of the First Cell Expression Matrix (Exp1.1.R
)
- Main Codes
- Test 1.1.1
- Test 1.1.2
- Test 1.1.3
2. Adapting countdc
to Seurat pipeline and generate clusters (Exp 1.2.R)
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⚠️ The workflows in the tutorial of Seurat vignette are adapted for this step: https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html
- But mitochondrial DNA percentage is not computed
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