Welcome to the GenoPop-Manual | GenoPop-Impute Overview | Population Genomics Metrics Overview | General Functionality | Metrics Overview | Installation Instructions for GenoPop | Prerequisites | Installing GenoPop from GitHub
Package: GenoPop 1.0.0
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_1.0.0.tar.gz
GenoPop_1.0.0.zip(r-4.7-any)GenoPop_1.0.0.zip(r-4.6-any)GenoPop_1.0.0.zip(r-4.5-any)
GenoPop_1.0.0.tgz(r-4.6-any)GenoPop_1.0.0.tgz(r-4.5-any)
GenoPop_1.0.0.tar.gz(r-4.7-any)GenoPop_1.0.0.tar.gz(r-4.6-any)
GenoPop_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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 from:2f04939366. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 289 | ||
| source / vignettes | OK | 223 | ||
| linux-release | OK | 289 | ||
| macos-release | OK | 267 | ||
| macos-oldrel | OK | 214 | ||
| windows-devel | OK | 268 | ||
| windows-release | OK | 179 | ||
| windows-oldrel | OK | 258 | ||
| wasm-release | OK | 118 |
Exports:calculateAlleleFreqsDxyFixedSitesFstGenoPop_ImputeHeterozygosityOneDimSFSPiPrivateAllelesSegregatingSitesseparateByPopulationsSingletonSitesTajimasDTwoDimSFSWattersonsTheta
Dependencies:BHBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayondigestdoParalleldoRNGforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangesiteratorsitertoolslambda.rlatticeMatrixmissForestrandomForestrangerrbibutilsRcppRcppEigenRdpackRhtslibrngtoolsRsamtoolsS4VectorsSeqinfosnowXVector
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 |