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rehh
View on CRAN: Click
here
Download and install rehh package within the R console
Install from CRAN:
install.packages("rehh")
Install from Github:
library("remotes")
install_github("cran/rehh")
Install by package version:
library("remotes")
install_version("rehh", "3.2.2")
Attach the package and use:
library("rehh")
Maintained by
Alexander Klassmann
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2012-03-15
Latest Update: 2021-09-15
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) , has given rise to
several statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: 'iHS' (Voight 2006) for
detecting positive or 'Darwinian' selection within a single population as well as
'Rsb' (Tang 2007) and
'XP-EHH' (Sabeti 2007) , targeted
at differential selection between two populations.
Various plotting functions are included to facilitate
visualization and interpretation of these statistics.
How to cite:
Alexander Klassmann (2012). rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests. R package version 3.2.2, https://cran.r-project.org/web/packages/rehh. Accessed 14 Jun. 2025.
Previous versions and publish date:
1.0 (2012-03-15 15:39), 1.1 (2013-04-26 14:30), 1.11 (2013-08-26 16:18), 1.12 (2015-04-07 16:01), 1.13 (2015-05-13 19:55), 2.0.0 (2016-08-01 15:35), 2.0.1 (2016-10-25 20:47), 2.0.2 (2016-11-18 12:43), 2.0.3 (2019-02-04 13:20), 2.0.4 (2019-02-13 17:20), 3.0.0 (2019-07-09 14:00), 3.0.1 (2019-07-11 15:42), 3.1.0 (2020-03-04 11:10), 3.1.1 (2020-06-19 12:00), 3.1.2 (2020-07-17 12:30), 3.2.0 (2020-11-01 11:00), 3.2.1 (2020-11-09 23:10)
Other packages that cited rehh R package
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Other R packages that rehh depends,
imports, suggests or enhances
Complete documentation for rehh
Functions, R codes and Examples using
the rehh R package
Some associated functions: allelefurcation-class . as.newick . calc_candidate_regions . calc_ehh . calc_ehhs . calc_furcation . calc_haplen . calc_pairwise_haplen . calc_region_stats . calc_sfs_tests . data2haplohh . distribplot . extract_regions . freqbinplot . ftree-class . furcation-class . haplen-class . haplohh-class . haplohh2sweepfinder . haplohh_cgu_bta12 . ies2xpehh . ihh2ihs . ines2rsb . make.example.files . manhattanplot . plot.ehh . plot.ehhs . plot.furcation . plot.haplen . plot.haplohh . rehh-package . remove.example.files . scan_hh . scan_hh_full . subset.haplohh . update_haplohh .
Some associated R codes: as.newick.R . calc_candidate_regions.R . calc_ehh.R . calc_ehhs.R . calc_furcation.R . calc_haplen.R . calc_pairwise_haplen.R . calc_region_stats.R . calc_sfs_tests.R . data2haplohh.R . distribplot.R . extract_regions.R . freqbinplot.R . furcation-class.R . haplohh-class.R . haplohh2sweepfinder.R . ies2xpehh.R . ihh2ihs.R . ines2rsb.R . make.example.files.R . manhattanplot.R . plot.ehh.R . plot.ehhs.R . plot.furcation.R . plot.haplen.R . plot.haplohh.R . rehh.R . scan_hh.R . scan_hh_full.R . subset.haplohh.R . update_haplohh.R . Full rehh package functions and examples
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