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:Marie Gurke [aut, cre]

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'))

On CRAN:

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

2.70 score 6 scripts 225 downloads 15 exports 40 dependencies

Last updated 2 months agofrom:20b1cfa4a4. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 13 2024
R-4.5-win	OK	Oct 13 2024
R-4.5-linux	OK	Oct 13 2024
R-4.4-win	OK	Oct 13 2024
R-4.4-mac	OK	Oct 13 2024
R-4.3-win	OK	Oct 13 2024
R-4.3-mac	OK	Oct 13 2024

Exports:calculateAlleleFreqs Dxy FixedSites Fst GenoPop_Impute Heterozygosity OneDimSFS Pi PrivateAlleles SegregatingSites separateByPopulations SingletonSites TajimasD TwoDimSFS WattersonsTheta

Dependencies:askpass BH BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl digest doParallel doRNG foreach formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges iterators itertools jsonlite lambda.r mime missForest openssl R6 randomForest Rhtslib rngtools Rsamtools S4Vectors snow sys UCSC.utils XVector zlibbioc

GenoPop

Rendered fromGenoPop.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2024-09-12
Started: 2024-09-12

Citation

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