corehunter: Multi-Purpose Core Subset Selection

Core Hunter is a tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general. Core Hunter can construct cores based on genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many provided evaluation measures depending on the precise purpose of the core (e.g. high diversity, representativeness, or allelic richness). In addition, multiple measures can be simultaneously optimized as part of a weighted index to bring the different perspectives closer together. The Core Hunter library is implemented in Java 8 as an open source project (see <http://www.corehunter.org>).

AuthorHerman De Beukelaer [aut, cre], Guy Davenport [aut], Veerle Fack [ths]
Date of publication2017-02-20 19:15:04
MaintainerHerman De Beukelaer <herman.debeukelaer@gmail.com>
LicenseMIT + file LICENSE
Version3.1.0

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Files

corehunter
corehunter/inst
corehunter/inst/java
corehunter/inst/java/slf4j-nop-1.7.21.jar
corehunter/inst/java/corehunter-3.1.0.jar
corehunter/inst/java/LICENSE
corehunter/inst/java/NOTICE
corehunter/inst/extdata
corehunter/inst/extdata/phenotypes.csv
corehunter/inst/extdata/genotypes.csv
corehunter/inst/extdata/distances.csv
corehunter/inst/extdata/genotypes-frequency.csv
corehunter/inst/extdata/genotypes-biparental.csv
corehunter/tests
corehunter/tests/test.R
corehunter/tests/testthat
corehunter/tests/testthat/testUtils.R
corehunter/tests/testthat/data
corehunter/tests/testthat/data/phenotypes-unknown-type.csv
corehunter/tests/testthat/data/genotypes-small.csv
corehunter/tests/testthat/data/genotypes-bi-small.csv
corehunter/tests/testthat/data/genotypes-freq-small.csv
corehunter/tests/testthat/data/phenotypes-small.csv
corehunter/tests/testthat/data/distances-small.txt
corehunter/tests/testthat/data/phenotypes-no-types.csv
corehunter/tests/testthat/testAnalysis.R
corehunter/tests/testthat/testExecution.R
corehunter/tests/testthat/testData.R
corehunter/NAMESPACE
corehunter/NEWS.md
corehunter/R
corehunter/R/execution.R corehunter/R/analysis.R corehunter/R/java.R corehunter/R/data.R corehunter/R/corehunter.R corehunter/R/zzz.R
corehunter/README.md
corehunter/MD5
corehunter/java
corehunter/java/README.txt
corehunter/DESCRIPTION
corehunter/man
corehunter/man/sampleCore.Rd corehunter/man/exampleData.Rd corehunter/man/distances.Rd corehunter/man/objective.Rd corehunter/man/genotypes.Rd corehunter/man/phenotypes.Rd corehunter/man/coreHunterData.Rd corehunter/man/getAlleleFrequencies.Rd corehunter/man/read.autodelim.Rd corehunter/man/wrapData.Rd corehunter/man/evaluateCore.Rd corehunter/man/getNormalizationRanges.Rd corehunter/man/corehunter.Rd corehunter/man/setRange.Rd
corehunter/LICENSE

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