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State Estimation
Example results
Cell type query
Gene lists
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Terms of use
Results for query id test_tabula-muris-lung
Data stats
Results are available:
Data downloads
Cell Type Report
Pre-processed cells
Post-processed cells
Cluster means
Label heatmap
Dendrogram
Genes
Gene correlation heatmap
Colormap 1:
Cluster
Lung_cell_types
test1
Cell type report
cellmesh_cluster_labels
Colormap 2:
Cluster
Lung_cell_types
test1
Cell type report
cellmesh_cluster_labels
Submit
Selected genes:
Log-transform data:
Normalize by gene:
Submit
Selected genes 1:
Selected genes 2:
Selected cluster:
All cells
Submit
Selected genes 1:
Selected genes 2:
Cluster 1:
Cluster 2:
P-value
Difference of correlations
Submit
Download plot as svg
Download plot data as table
Cell labels:
Cluster
Entropy
Gene
Cluster weights
Read counts
Lung_cell_types
test1
Cell type report
cellmesh_cluster_labels
Upload cell labels
Custom cell selection
Cluster ID:
Submit
Gene name:
Raw data
Post-processed
Submit
Upload color track here
Type of color track:
Continuous
Discrete
Table
Submit
Custom label:
New label
Label name:
Label color (optional):
Selection type:
Cluster
Selection
Gene
Lung_cell_types
test1
Cell type report
cellmesh_cluster_labels
=
!=
Delete
New criterion - AND
New criterion - OR
Submit
Get cell/cluster info
Recluster
Reanalyze
Re-run pipeline
Run batch effect correction
Copy dataset
Sub-select cells
Sub-select clusters
Re-run clustering
Split clusters
Merge clusters
Create new cluster
Delete cells
×
Clustering options
Argmax
Leiden
Louvain
Leiden_baseline
Top genes (1-vs-rest fold change)
Top genes (p-value of 1-vs-rest fold change)
Pairwise fold change
Pairwise p-value
Pairwise volcano plot
Violin plots for a gene
Highly expressed genes
Double-pair comparison
Top clusters by mean value for the given gene
Top clusters by nonzero proportion
Cluster 1:
Cluster 2:
Cluster 1:
Cluster 2:
Cluster 3:
Cluster 4:
Genes of interest (optional):
Submit
Use log-transform:
Use all clusters:
Number of top genes:
Download plot as svg
Gene set query
Cell similarity search
History
Gene set queries
Currently selected top genes:
Top genes go here
Database:
Enrichr
CellMarker
CellMeSH
CellMeSH-Anatomy
Gene Ontology
Bacillus subtilis
KEGG Pathways
Call Enrichr on selected genes
Gene set:
Human_Gene_Atlas
Mouse_Gene_Atlas
Allen_Brain_Atlas_up
ARCHS4_Tissues
ARCHS4_Cell-lines
GO_Biological_Process_2017
GO_Cellular_Component_2017
GO_Molecular_Function_2017
Jensen_COMPARTMENTS
Jensen_DISEASES
Jensen_TISSUES
KEGG_2016
Reactome_2016
Submit Enrichr query
Query CellMarker with selected genes
Statistical test:
Hypergeometric test
Species:
All
Homo sapiens
Mus musculus
Cells or tissues:
Cells
Tissues
Submit CellMarker query
Query CellMeSH with selected genes
Statistical test:
Hypergeometric test
Normalized Hypergeometric test
Probabilistic model
GSVA
Species:
Homo sapiens
Mus musculus
Human + mouse
C. Elegans
Submit CellMesh query
Query CellMeSH with selected genes
Statistical test:
Hypergeometric test
Normalized Hypergeometric test
Probabilistic model
GSVA
Species:
Homo sapiens
Mus musculus
Human + mouse
C. Elegans
MeSH root (optional):
Submit CellMesh Anatomy query
Query GO with selected genes
Species:
Homo sapiens
Mus musculus
FDR Threshold:
Submit GO query
Query Subtiwiki with selected genes
Subtiwiki category:
Gene categories
Regulons
Operons
All
Gene Info
Submit Subtiwiki query
Query GO with selected genes
Species:
Homo sapiens
Mus musculus
Both
Submit KEGG query
Cell similarity search
Database:
Tabula Muris
Allen Brain Atlas neocortex
Method:
Spearman
Cluster:
Submit
History
