CellSeekr

CellSeekr Gene × Phenotype — DE — UMAP

Matosevic Lab CellSeekr Home Page

Gene × Phenotype Analysis Top 50 DE Gene Finder UMAP Viewer

Signature to Cell Tethering

Top 50 DE Genes

UMAP Viewer

Proximity Mapper

Geo Cluster Explorer

Targeted

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Tumor / Dataset:

Pairwise Comparison:

Proportional Expression per Cell Type and Ranking Leaderboard

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Significance Leaderboard - Proportion of Cell Types Expressing Each Gene Compared Between Groups

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Phenotype Gate

Cells must pass this gate before DE testing.

Optional + Gate

Restrict to gene+ or gene- cells before DE.

+ -

Top N per direction: 50

Min detection fraction: 0.05

Volcano label selection

Select which genes to label on the volcano plot.

UP genes to label:

DOWN genes to label:

Volcano Plot

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Download UP (.tsv)

Download DOWN (.tsv)

Phenotype Gate

Cells are filtered to this gate before plotting. Same logic as Mode A.

Genes to highlight

A cell lights up if ANY gene is expressed > 0.

0 genes

Display options

Highlight color

Point size

Label cluster centroids

Download PDF

Query Gene (+/−):

+ -

Query cell type:

Reference A Gene (+/−):

+ -

Reference A cell type:

Reference B Gene (+/−):

+ -

Reference B cell type:

Phenotype Gate

Filter cells before sampling. Only cells passing this gate enter the distance computation. Same logic as Mode A / UMAP Viewer.

Sampling

500 cells from each group (1 000 total) are sampled for geometric clustering. All remaining cells are then assigned via Seurat-cluster majority vote.

Groups

Driven by the shared pairwise selector at the top of the page.

Display

Point size (background cells)

Point size (seed cells)

Overlay seed cells with black border

Cells per group to sample

Geo-Cluster DE Filters

Applied to pairwise gene tables below the UMAP. Genes must pass BOTH thresholds to appear.