Package: GenoPop 0.9.3
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:
GenoPop_0.9.3.tar.gz
GenoPop_0.9.3.zip(r-4.5)GenoPop_0.9.3.zip(r-4.4)GenoPop_0.9.3.zip(r-4.3)
GenoPop_0.9.3.tgz(r-4.4-any)GenoPop_0.9.3.tgz(r-4.3-any)
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)
| # Install 'GenoPop' in R: |
| install.packages('GenoPop', repos = c('https://migurke.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:20b1cfa4a4. Checks:OK: 6 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 12 2024 |
| R-4.5-win | OK | Nov 12 2024 |
| R-4.5-linux | WARNING | Nov 12 2024 |
| R-4.4-win | OK | Nov 12 2024 |
| R-4.4-mac | OK | Nov 12 2024 |
| R-4.3-win | OK | Nov 12 2024 |
| R-4.3-mac | OK | Oct 13 2024 |
Exports:calculateAlleleFreqsDxyFixedSitesFstGenoPop_ImputeHeterozygosityOneDimSFSPiPrivateAllelesSegregatingSitesseparateByPopulationsSingletonSitesTajimasDTwoDimSFSWattersonsTheta
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurldigestdoParalleldoRNGforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesiteratorsitertoolsjsonlitelambda.rmimemissForestopensslR6randomForestRhtslibrngtoolsRsamtoolsS4VectorssnowsysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dxy | Dxy |
| FixedSites | FixedSites |
| Fst | Fst |
| GenoPop-Impute | GenoPop_Impute |
| Heterozygosity Rate | Heterozygosity |
| OneDimSFS | OneDimSFS |
| Pi | Pi |
| PrivateAlleles | PrivateAlleles |
| SegregatingSites | SegregatingSites |
| SingletonSites | SingletonSites |
| TajimasD | TajimasD |
| TwoDimSFS | TwoDimSFS |
| WattersonsTheta | WattersonsTheta |
