Package: GenoPop 0.9.3

Marie Gurke

GenoPop: Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files

Tools for efficient processing of large, whole genome genotype data sets in variant call format (VCF). It includes several functions to calculate commonly used population genomic metrics and a method for reference panel free genotype imputation, which is described in the preprint Gurke & Mayer (2024) <doi:10.22541/au.172515591.10119928/v1>.

Authors:Marie Gurke [aut, cre]

GenoPop_0.9.3.tar.gz
GenoPop_0.9.3.tar.gz(r-4.5-noble)GenoPop_0.9.3.tar.gz(r-4.4-noble)
GenoPop_0.9.3.tgz(r-4.4-emscripten)GenoPop_0.9.3.tgz(r-4.3-emscripten)
GenoPop.pdf |GenoPop.html✨
GenoPop/json (API)

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This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

15 exports 0.09 score 40 dependencies 6 scripts 4 downloads

Last updated 6 days agofrom:20b1cfa4a4. Checks:OK: 2. Indexed: yes.

Exports:calculateAlleleFreqsDxyFixedSitesFstGenoPop_ImputeHeterozygosityOneDimSFSPiPrivateAllelesSegregatingSitesseparateByPopulationsSingletonSitesTajimasDTwoDimSFSWattersonsTheta

Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurldigestdoParalleldoRNGforeachformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesiteratorsitertoolsjsonlitelambda.rmimemissForestopensslR6randomForestRhtslibrngtoolsRsamtoolsS4VectorssnowsysUCSC.utilsXVectorzlibbioc