Package: rehh
Maintainer: Alexander Klassmann <rehh@oneoverx.eu>
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Version: 3.1.2
License: GPL (>= 2)
Title: Searching for Footprints of Selection using 'Extended Haplotype
        Homozygosity' Based Tests
Description: Population genetic data such as 'Single Nucleotide
        Polymorphisms' (SNPs) is often used to identify genomic regions
        that have been under recent natural or artificial selection
        and might provide clues about the molecular mechanisms of adaptation. 
        One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), 
        introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to 
        several statistics designed for whole genome scans. 
        The package provides functions to compute three of these,
        namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
        detecting positive or 'Darwinian' selection within a single population as well as
        'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 
        'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted
        at differential selection between two populations. 
        Various plotting functions are also included to facilitate
        visualization and interpretation of these statistics. 
        Due to changes in the API, albeit mostly minor, 
        versions 3.X are not compatible with versions 2.0.X.
        Note: optionally, vcf files can be imported using package vcfR. That package
        is currently removed from CRAN, but can still be installed from 
        <https://github.com/knausb/vcfR> following instructions there.
Depends: R (>= 2.10)
Imports: methods, rehh.data
Suggests: ape, bookdown, data.table, gap, knitr, qqman, rmarkdown,
        R.utils, testthat, vcfR
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2020-07-17 09:16:17 UTC; alex
RoxygenNote: 7.1.0
URL: https://CRAN.R-project.org/package=rehh,
        https://gitlab.com/oneoverx/rehh
BugReports: https://gitlab.com/oneoverx/rehh/issues
Repository: CRAN
Date/Publication: 2020-07-17 10:30:03 UTC
Built: R 4.0.2; x86_64-w64-mingw32; 2020-08-02 06:43:36 UTC; windows
Archs: i386, x64
