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Welcome to the Gene Expression Deconvolution Interactive Tool! This open-source app allows you to deconvolve gene expression data into cell type fractions in seconds, without the need for expensive flow cytometry. To get started, upload your expression data and select a reference. For more information, read the paper here.

This is the development version of GEDIT 3.0. Please report any bugs to miastay@ucla.edu.

1

Select mixture

Select an expression dataset with an unknown cell type mixture

Upload a gene expression matrix where the first column is gene symbols and the first row is sample names. See an example input file here.

2

Choose reference

Select a reference matrix of cell types to compute against

Tabula Sapiens

24 human tissues

LM22

Newman et al

ImmunoStates

Vallania et al

Blueprint

Martens and Stunnenberg

ENCODE

ENCODE Project Consortium

Human Body Atlas

Su et al

Skin Signatures

Swindell et al

Human Primary Cell Atlas

Mabbott et al

3

Configure run

Analysis Options

Ranking Metric

Minimum entropy Z-score

Row Scaling

Signature Genes per Cell Type

Heatmap Options

Colormap

Clustering

Rows Columns

Miscellaneous

Show cell values?

Draw cell outlines?

Square cells?

Orientation

Samples as columns Cells as columns

4

Results

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1