V-SVA: A Shiny app for Visual Surrogate Variable Analysis
Guided Tutorial!
Download Tutorial
Download Test Expression
Download Test Metadata
1. Load Data
(Required) Choose gene/ADT file to upload
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Do You Have Sample Metadata?
Yes
No
(Optional) Choose sample metadata file to upload
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2a. Cell/Sample Filtering (Optional)
Filter Cells/Samples?
Yes
No
Minimum Genes Detected in each Cell
Run Cell Filtering
2b. Down-sample Cells (Optional)
Down-sample?
Yes
No
Minimum number of cells
Run Cell Down-sampling
2c. Gene Filtering and Normalization (Optional)
Filter Genes?
Yes
No
# of Feature Counts in each Cell
Feature Detected in # of Cells
Normalization Method
CPM
Quantile
scran
None
Run Gene Filtering
3. Specify Known Factors to Adjust For
Known Factors
4. SVA Analysis
SVA Method
IA-SVA
SVA
ZINB-WaVE
Parameter Choice
Percentage Threshold
Number of SVs
% Threshold for SV retention
Number of SVs to Estimate
Number of SVs to Estimate
Number of Latent Factors to Estimate
Run Analysis
Author/Contact:
Nathan Lawlor
Questions/Issues?:
Visit the App Github Page Here!
Other Resources:
Visit the Ucar Lab Here!
Data/QC
Surrogate Variables
Pairwise Surrogate Variable
Identify Marker Genes
Visualization with Marker Genes
Gene Enrichment Analysis
Download a Report of Code Used
Download Histogram
Graphing Options
Color Points
SV's to Plot
Update Plots
Correlation Plot
Download Correlation Plot
Download Correlation Table
Surrogate Variables Plot
Download SV Plot
Download SV Table
Download Pairwise Plot
Color Points
SV X-axis
SV Y-axis
Update Pairwise SV Plot
Choose SVs
P-Value Adjustment
BH
bonferroni
none
Adjusted P-value cutoff
R-squared cutoff
Known Factors to Include in Heatmap
Identify Marker Genes
Download Heatmap
Marker Genes Table:
Download Marker Genes Table
Dimension Reduction
PCA
t-SNE
Classical Metric MDS
Color Points
Run Dimension Reduction Analysis
Update Plot Point Colors
Download All Genes Plot
Download All Genes Coordinates
Download Marker Genes Plot
Download Marker Genes Coordinates
Species
Homo sapiens
Mus musculus
Rattus norvegicus
Enrichment Analysis Type
Gene Ontology Biological Process
Gene Ontology Cellular Component
Gene Ontology Molecular Function
KEGG
Homo sapiens Immune Modules
Homo sapiens PBMC Cell Specific Modules
Homo sapiens Cell Cycle Genes
Custom
Enrichment Analysis Type
Gene Ontology Biological Process
Gene Ontology Cellular Component
Gene Ontology Molecular Function
KEGG
Mus musculus Cell Cycle Genes
Custom
Enrichment Analysis Type
Gene Ontology Biological Process
Gene Ontology Cellular Component
Gene Ontology Molecular Function
KEGG
Rattus norvegicus Cell Cycle Genes
Custom
Upload custom gene and module file
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Upload custom module identifier file
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P-value cutoff
P-value Adjustment
BH
bonferroni
none
Adjusted P-value cutoff
Max # of Results to Visualize
Run Enrichment Analysis
Download Enrichment Analysis Plot
Gene Enrichment Analysis Table
Download Enrichment Analysis Results Table
Generate report
