OEFinder specifications

Unique identifier:
Command line interface, Graphical user interface
Input data:
OEFinder requires a genes-by-cells expression matrix. The expression matrix can be either normalized or unnormalized. If the input matrix is unnormalized, OEFinder applies the Median-by-Ratio normalization method introduced by Anders and Huber (2010) prior to OE detection.
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Software type:
Restrictions to use:
Output data:
(i) List of OE genes: OEFinder outputs two .csv files - one contains a sorted list of OE genes and the other contains p-values for all genes, (ii) Expression matrix for downstream analysis: OEFinder outputs a normalized expression matrix that can be directly input to downstream analyses. The user has the option to choose either removal of the OE genes, or imputation of the OE genes with adjusted values and (iii) visualization of OE genes: OEFinder generates a .pdf file contains expression plots of the top N OE genes, where N is user-specified.
Programming languages:


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OEFinder support



  • Ron Stewart <>


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Morgridge Institute for Research, Madison, WI, USA; Department of Statistics, University of Wisconsin, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA

Funding source(s)

This work was funded in part by GM102756, 4UH3TR000506, 5U01HL099773, Charlotte Geyer Foundation and Morgridge Institute for Research.

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