OEFinder specifications

Information


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

Versioning


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Documentation


Maintainer


  • person_outline Ron Stewart <>

Publication for OEFinder

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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