OEFinder statistics

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Associated diseases

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OEFinder specifications


Unique identifier OMICS_09784
Name OEFinder
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
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.
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.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Ron Stewart <>

Publication for OEFinder

OEFinder in publications

PMCID: 5030210
PMID: 27708664
DOI: 10.3389/fgene.2016.00163

[…] provides calibration of the relative amount of starting material (brennecke et al., ; treutlein et al., )., recently, specific methods have been developed to filter genes from scrna-seq dataset. oefinder is designed to identify artifact genes from scrna-seq experiments using the fluidigm c1 platform for cell capture (leng et al., ). for experiments that quantify gene expression with umi […]

PMCID: 4823857
PMID: 27052890
DOI: 10.1186/s13059-016-0927-y

[…] masking the effects that are of interest, the oscillatory gene groups identified by oscope may be used subsequently in a de-noising step, using either sclvm or, for specific groups of genes, oefinder []. it should be noted that oscope is useful not only when oscillators are nuisance variables but also when they are of direct interest. for example, oscope could be used in studies that aim […]

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OEFinder institution(s)
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
OEFinder 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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