polyploids r-universe repositoryhttps://polyploids.r-universe.devPackage updated in polyploidscranlike-server 0.11.53https://github.com/polyploids.png?size=400polyploids r-universe repositoryhttps://polyploids.r-universe.devMon, 26 Sep 2022 01:09:07 GMT[polyploids] polyRAD 1.6.0.9003Lindsay.Clark@seattlechildrens.org (Lindsay V. Clark)Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis. 'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.https://github.com/r-universe/polyploids/actions/runs/3124906921Mon, 26 Sep 2022 01:09:07 GMTpolyRAD1.6.0.9003successhttps://polyploids.r-universe.devhttps://github.com/lvclark/polyRADpolyRADtutorial.RmdpolyRADtutorial.htmlpolyRAD Tutorial2018-06-08 22:10:382022-04-04 16:04:07isolocus_sorting.Rmdisolocus_sorting.htmlVariant and Genotype Calling in Highly Duplicated Genomes2019-11-03 16:30:472022-03-28 14:06:20[polyploids] polyBreedR 0.27endelman@wisc.edu (Jeffrey Endelman)Genomics-assisted breeding for polyploids (and diploids)https://github.com/r-universe/polyploids/actions/runs/3075085385Sat, 17 Sep 2022 22:17:12 GMTpolyBreedR0.27successhttps://polyploids.r-universe.devhttps://github.com/jendelman/polyBreedRVignette1.RmdVignette1.htmlpolyBreedR Vignette12020-07-20 01:56:522021-07-30 22:27:20Vignette2.RmdVignette2.htmlpolyBreedR Vignette22020-07-20 01:56:522021-03-09 01:19:16[polyploids] qtlpoly 0.2.4gdesiqu@ncsu.edu (Gabriel de Siqueira Gesteira)Performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. (2020) <doi:10.1534/genetics.120.303080>.https://github.com/r-universe/polyploids/actions/runs/3121067025Fri, 26 Aug 2022 15:23:44 GMTqtlpoly0.2.4successhttps://polyploids.r-universe.devhttps://github.com/gabrielgesteira/QTLpoly[polyploids] mappoly 0.3.1mmollin@ncsu.edu (Marcelo Mollinari)Construction of genetic maps in autopolyploid full-sib populations.
Uses pairwise recombination fraction estimation as the first
source of information to sequentially position allelic variants
in specific homologues. For situations where pairwise analysis has
limited power, the algorithm relies on the multilocus likelihood
obtained through a hidden Markov model (HMM). For more detail,
please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378>
and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.https://github.com/r-universe/polyploids/actions/runs/3117345768Thu, 25 Aug 2022 14:16:23 GMTmappoly0.3.1successhttps://polyploids.r-universe.devhttps://github.com/mmollina/MAPpolymappoly_startguide.Rmdmappoly_startguide.htmlmappoly_intro2022-05-23 23:52:302022-07-05 18:50:40[polyploids] viewpoly 0.3.0chtaniguti@tamu.edu (Cristiane Taniguti)Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly' and 'polyqtlR' packages.https://github.com/r-universe/polyploids/actions/runs/3055131978Fri, 19 Aug 2022 17:25:19 GMTviewpoly0.3.0successhttps://polyploids.r-universe.devhttps://github.com/mmollina/viewpoly[polyploids] updog 2.1.3gerard.1787@gmail.com (David Gerard)Implements empirical Bayes approaches to genotype
polyploids from next generation sequencing data while
accounting for allele bias, overdispersion, and sequencing
error. The main functions are flexdog() and multidog(),
which allow the specification
of many different genotype distributions. Also provided are functions to
simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as
functions to calculate oracle genotyping error rates, oracle_mis(), and
correlation with the true genotypes, oracle_cor(). These latter two
functions are useful for read depth calculations. Run
browseVignettes(package = "updog") in R for example usage. See
Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and
Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details
on the implemented methods.https://github.com/r-universe/polyploids/actions/runs/2983370048Thu, 04 Aug 2022 18:06:24 GMTupdog2.1.3successhttps://polyploids.r-universe.devhttps://github.com/dcgerard/updogsmells_like_updog.Rmdsmells_like_updog.htmlExample Use of Updog2018-05-04 19:29:532020-02-27 18:55:33multidog.Rmdmultidog.htmlGenotyping Many SNPs with multidog()2019-12-05 21:14:332021-01-21 15:16:41oracle_calculations.Rmdoracle_calculations.htmlOracle Calculations2018-05-11 17:26:452020-02-27 18:55:33simulate_ngs.Rmdsimulate_ngs.htmlSimulate Next-Generation Sequencing Data2018-05-04 20:14:382020-02-27 18:55:33[polyploids] diaQTL 1.08endelman@wisc.edu (Jeffrey Endelman)QTL analysis of diploid and autotetraploid diallel populations. Phenotypes are regressed on genotype probabilities, and the regression coefficients are random effects.https://github.com/r-universe/polyploids/actions/runs/3076334796Wed, 20 Jul 2022 15:26:17 GMTdiaQTL1.08successhttps://polyploids.r-universe.devhttps://github.com/jendelman/diaQTLdiaQTL_vignette.RmddiaQTL_vignette.htmldiaQTL Vignette2021-04-27 00:46:032021-06-01 22:28:19[polyploids] GWASpoly 2.11endelman@wisc.edu (Jeffrey Endelman)Designed for genome-wide association studies in autopolyploids.https://github.com/r-universe/polyploids/actions/runs/2969164841Wed, 04 May 2022 18:02:00 GMTGWASpoly2.11failurehttps://polyploids.r-universe.devhttps://github.com/jendelman/GWASpoly[polyploids] polyqtlR 0.0.9pbourkey@gmail.com (Peter Bourke)Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in
autopolyploid bi-parental F1 populations.
For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated.
Significance thresholds, exploring QTL allele effects and visualising results are provided.
For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.https://github.com/r-universe/polyploids/actions/runs/2961849866Wed, 02 Feb 2022 15:40:02 GMTpolyqtlR0.0.9successhttps://polyploids.r-universe.devhttps://github.com/cran/polyqtlRpolyqtlR_vignette.rmdpolyqtlR_vignette.htmlHow to use polyqtlR2020-12-16 09:40:022022-02-02 15:40:02[polyploids] PolyHaplotyper 1.0.1roeland.voorrips@wur.nl (Roeland E. Voorrips)Infer the genetic composition of individuals
in terms of haplotype dosages for a haploblock, based
on bi-allelic marker dosages, for any ploidy level.
Reference: Voorrips and Tumino: PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.
Submitted to BMC Bioinformatics (2021).https://github.com/r-universe/polyploids/actions/runs/3026843192Thu, 17 Jun 2021 13:20:05 GMTPolyHaplotyper1.0.1successhttps://polyploids.r-universe.devhttps://github.com/cran/PolyHaplotyperPolyHaplotyper.RmdPolyHaplotyper.htmlPolyHaplotyper vignette2021-02-10 09:40:322021-02-10 09:40:32[polyploids] polymapR 1.1.2pbourkey@gmail.com (Peter Bourke)Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (submitted, 2020).https://github.com/r-universe/polyploids/actions/runs/2962008470Tue, 09 Mar 2021 14:20:02 GMTpolymapR1.1.2successhttps://polyploids.r-universe.devhttps://github.com/cran/polymapRVignette_polymapR.RmdVignette_polymapR.htmlHow to use polymapR2017-12-05 17:39:062021-03-09 14:20:02Vignette_genotype_probabilities.RmdVignette_genotype_probabilities.htmlUsing genotype probabilities in polymapR2020-07-15 21:30:082021-03-09 14:20:02[polyploids] fitPoly 3.0.0roeland.voorrips@wur.nl (Roeland E. Voorrips)Genotyping assays for bi-allelic markers (e.g. SNPs) produce
signal intensities for the two alleles. 'fitPoly' assigns genotypes
(allele dosages) to a collection of polyploid samples based on these
signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was
limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any
ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011)
<doi:10.1186/1471-2105-12-172>.https://github.com/r-universe/polyploids/actions/runs/3096185087Fri, 16 Mar 2018 18:01:05 GMTfitPoly3.0.0successhttps://polyploids.r-universe.devhttps://github.com/cran/fitPoly