A Minimal Book Example
1
Preface
Process Analysis
2
Seurat Pre-process
2.1
Load count matrix from CellRanger
2.1.1
Quality control by visualization
2.2
Cell-level filtering
2.3
Merge individuals
2.4
Normalize, scale, find variable genes and dimension reduciton
3
Find Doublet using Scrublet
3.1
description
3.2
input data
3.3
process
3.4
output
Visualize
4
Seurat QC Cell-level Filtering
4.1
Description
4.2
Load seurat object
4.3
Add other meta info
4.4
Violin plots to check
5
Scrublet Doublet Validation
5.1
Description
5.2
Load seurat object
5.3
Validate the doublet prediction
5.4
Calculate factions of doublet per cluster
5.5
Explore the component clusters for doublets by DEG
5.6
Explore the component clusters for doublets by canonical gene
6
Seurat Individual Batch Effect Exploration
6.1
Descripiton
6.2
Load seurat object
6.3
Explore individual distribution by
Dimplot
6.4
Calculate individual distribution per cluster with different resolution
7
Assign Gene Signature
7.1
Description
7.2
Load seurat object
7.3
Load gene lists, here using the layer-enriched genes as examples
7.4
Calcuate gene signature per gene list
7.5
Explore the gene signature by
FeaturePlot
and
VlnPlot
8
Stacked Vlnplot for Given Features Sets
8.1
Descripiton
8.2
Load seurat object
8.3
Source stacked vlnplot funciton
8.4
Stacked Vlnplot given gene set
8.5
Descripiton
8.6
Load seurat object
8.7
ColorPalette for heatmap
8.8
ColorPalette for discreate groups
Published with bookdown
Single Cell Multi-Omics Data Analysis
Visualize