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CAPE specifications


Unique identifier OMICS_10122
Alternative name Combined Analysis of Pleiotropy and Epistasis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.2
Stability Stable
stats, RColorBrewer, parallel, graphics, Matrix, utils, grDevices, corpcor, foreach, igraph, doParallel, fdrtool, qpcR, shape, R(≥3.2.2), evd, HardyWeinberg, regress
Maintained Yes


No version available



  • person_outline Gregory W. Carter

Publication for Combined Analysis of Pleiotropy and Epistasis

CAPE citations


Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs

PLoS One
PMCID: 5739412
PMID: 29267314
DOI: 10.1371/journal.pone.0189669

[…] epistasis in the modulation of quantitative traits while other studies have shown nonsignificant contribution []. Results of the multi-trait model were supported by further genetic analysis based on combined analysis of pleiotropy and epistasis which showed various patterns of genetic interactions among markers and traits. The marker-to-trait effect revealed that grain yield was enhanced by marke […]


Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice

PMCID: 5499176
PMID: 28592500
DOI: 10.1534/genetics.116.198051

[…] seq data were batch corrected and further processed to produce the inputs used for epistasis inference. Third, we developed and applied a multi-parent version of our previously described software for combined analysis of pleiotropy and epistasis (CAPE). This analysis pipeline combines information across multiple traits to infer directed epistasis between genetic variants. Fourth, we further interp […]


Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross

PLoS Genet
PMCID: 4734753
PMID: 26828925
DOI: 10.1371/journal.pgen.1005805

[…] Assessing genetic interactions and their relation to multiple phenotypes provides an overall picture of the genetic network regulating BMD and related phenotypes. We used a recently developed method, Combined Analysis of Pleiotropy and Epistasis (CAPE) [], to integrate information across multiple phenotypes to infer directed genetic interactions between loci.We integrated genetic interactions infl […]


A Genetic Interaction Network Model of a Complex Neurological Disease

PMCID: 4241132
PMID: 25251056
DOI: 10.1111/gbb.12178

[…] rait requires the use of novel analytical strategies that specifically address genetic interactions.Here we investigate genetic interactions influencing SWD in mice using a novel algorithm called the Combined Analysis of Pleiotropy and Epistasis (CAPE) (; ). We combined three populations of mice, each with one mutation causing genetically complex SWD – Gria4, Scn8a, or Gabrg2. Gria4 encodes one of […]


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CAPE institution(s)
The Jackson Laboratory, Bar Harbor, ME, USA
CAPE funding source(s)
NIGMS grants K25 GM079404 and P50 GM076468; NCI grant CA034196; the Howard Hughes Medical Institute and the Hearst Endowment

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