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Overview Plots
Embedding
Embedding
Size of Points in UMAP
Dimension 1
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Dimension 2
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Variable to Plot
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
Embedding
Embedding
Size of Points in UMAP
Dimension 1
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Dimension 2
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Variable to Plot
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
Histogram (Read Counts, etc.)
Resolution of clustering algorithm (affects number of clusters)
Y axis transforamtion
log
linear
Histogram (Read Counts, etc.)
Resolution of clustering algorithm (affects number of clusters)
Y axis transforamtion
log
linear
Selected Cells
Clustering Tree
Violin Plots
Gene or transcript expression by which to color the plot eg. 'NRL' or 'ENST00000488147'
Data Type
transformed
raw counts
Download
Heatmap
Data Scaling
scaled
unscaled
Clustering algorithm or metadata for column arrangement
Plot Heatmap
Download Heatmap
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
Plot Coverage
Select a Gene
Color by Variable
Plot Coverage
Download Coverage Plot
Collapse Introns
Summarize Coverage to Mean
Summarize transcript models to gene
Scale Y Axis
absolute
log10
start coordinate
end coordinate
Reformat Metadata
Header
Choose CSV File of metadata with cell names in first column
Browse...
Update Metadata
Update By:
table (below)
uploaded file
Subset Object Input
Embedding
Embedding
Size of Points in UMAP
Dimension 1
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Dimension 2
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Variable to Plot
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
Subset Settings
reset object to initial state
subset object by selected cells
subset object by uploaded csv
Upload .csv file with cells to include
Browse...
Selected Cells
Find Markers
Find Markers
Resolution of clustering algorithm (affects number of clusters)
Select Number of Markers to Plot for Each Value
Method of Marker Selection
wilcox
P Value cutoff
Feature for Marker Plot
Plot Markers!
Download Markers!
Make Markers Unique
Hide Pseudogenes
Embedding
Embedding
Size of Points in UMAP
Dimension 1
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Dimension 2
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Variable to Plot
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
All Transcripts
Embedding
Embedding
Size of Points in UMAP
Dimension 1
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Dimension 2
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Variable to Plot
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
Transcript Expression per Gene
Gene or transcript expression by which to color the plot; eg. 'NRL'
Transcript to Plot
Download Transcript Plots
Embedding
Transcript Expression per Gene
Gene or transcript expression by which to color the plot; eg. 'NRL'
Group by:
Plot transcript composition
Standardize Expression
Drop Zero Values
Differential Expression
Embedding
Embedding
Size of Points in UMAP
Dimension 1
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Dimension 2
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Variable to Plot
Gene or transcript expression by which to color the plot; eg. 'NRL' or 'ENST00000488147'
Differential Expression Settings
Cells to Compare
SingleCellExperiment Cluster
Custom Selection
Resolution of clustering algorithm (affects number of clusters)
first cluster to compare
second cluster to compare
Resolution of clustering algorithm (affects number of clusters)
Save to Custom Cluster 1
Save to Custom Cluster 2
Features to Compare
gene
transcript
Run Differential Expression
Download Complete DE Results
Volcano Plot
FC cutoff value (log2 fold change)
-log10 p adj value
Download Volcano Plot
Selected Cells
Custom Cluster 1
Custom Cluster 2
Regress Features
Regress Objects By Genes
Technical Information
Information about samples and analysis