OncoNEM specifications


Unique identifier OMICS_12092
Name OncoNEM
Alternative name Oncogenetic Nested Effects Model
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The inputs to OncoNEM are (1) a binary genotype matrix containing the observed genotypes of every cell at every SSNV locus and (2) the false positive rate (FPR) α and false negative rate (FNR) β, which can be estimated from data.
Output data The OncoNEM output includes (1) inferred tumor subpopulations, (2) a tree describing evolutionary relationships between these subpopulations and (3) posterior probabilities of the occurrence of mutations.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Florian Markowetz <>

Publication for Oncogenetic Nested Effects Model

OncoNEM institution(s)
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
OncoNEM funding source(s)
This work was funded by CRUK core grant C14303/A17197.

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