CiteFuse
Analysis
Reference
Example
Upload .rds file (SingleCellExperiment Object)
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Dimension reduction
Dimension reduction method
UMAP
tSNE
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Fusion and clustering analysis
Clustering algorithm
Spectral clustering
Louvain clustering
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Differential expression analysis
DE method
wilcox test
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ADT evaluation
Calculating ADT importance scores
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Gene/ADT Scatter Plots
Reduced Dimension Plots
Correlation Heatmap
Gene-ADT Correlation Network
3D Scatter Plot
DE - circlepackPlot
DE - results
DE - heatmap
ADT evaluation plots
Umap Plots:
UMAP using RNA expression
UMAP using ADT expression
Colour by
none
Modality of Feature 1
RNA
ADT
Select Gene 1
Select ADT 1
Modality of Feature 2
RNA
ADT
Select Gene 2
Select ADT 2
Download Plot
Colour by
none
RNA
ADT
Select Gene
Select ADT
Download Plot
Cells
All
Modality of X-axis
ADT
RNA
Select Gene (X-axis)
Select ADT (X-axis)
Modality of Y-axis
ADT
RNA
Select Gene (Y-axis)
Select ADT (Y-axis)
Download Plot
Cells
All
Correlation Threshold
Colour by
none
Modality of X-axis
ADT
RNA
Modality of Y-axis
ADT
RNA
Modality of Z-axis
ADT
RNA
Select Gene (X-axis)
Select ADT (X-axis)
Select Gene (Y-axis)
Select ADT (Y-axis)
Select Gene (Z-axis)
Select ADT (Z-axis)
circlepackPlot
Adjusted p-value
Number of top genes
Adjusted p-value
Number of top genes
Boxplot of ADT importance scores
CiteFuse is a comprehensive tool kit for the analysis of CITE-seq data
Github:
https://SydneyBioX.github.io/CiteFuse