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CAPE specifications
Information
| Unique identifier | OMICS_10122 |
|---|---|
| Name | CAPE |
| 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 |
| Requirements |
stats, RColorBrewer, parallel, graphics, Matrix, utils, grDevices, corpcor, foreach, igraph, doParallel, fdrtool, qpcR, shape, R(≥3.2.2), evd, HardyWeinberg, regress
|
| Maintained | Yes |
Versioning
No version available
Documentation
- Documentation: https://cran.r-project.org/web/packages/cape/cape.pdf
Maintainer
- person_outline Gregory W. Carter
Publication for Combined Analysis of Pleiotropy and Epistasis
CAPE citations
(4)Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs
[…] 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
[…] 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
[…] 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
[…] 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 […]
Citations
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