updog - Flexible Genotyping for Polyploids

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.

Last updated 12 months ago

8.85 score 25 stars 2 packages 79 scripts 384 downloads

mappoly - Genetic Linkage Maps in Autopolyploids

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 homologous chromosomes. 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>.

Last updated 9 months ago

polyploidpolyploid-genetic-mappingpolyploidy

7.98 score 25 stars 1 packages 107 scripts 329 downloads

polyRAD - Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

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>.

Last updated 11 months ago

bioinformaticsdna-sequencinggenotype-likelihoodsgenotyping-by-sequencinghacktoberfestrad-seqrad-sequencingsnp-genotyping

6.97 score 27 stars 87 scripts 303 downloads

qtlpoly - Random-Effect Multiple QTL Mapping in Autopolyploids

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>.

Last updated 9 days ago

polyploidqtl-mapping

5.33 score 6 stars 60 scripts 224 downloads

viewpoly - A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

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', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.

Last updated 11 months ago

4.38 score 4 stars 2 scripts 186 downloads

diaQTL - QTL Analysis in Diallel Populations

QTL analysis of diploid and autotetraploid diallel populations. Phenotypes are regressed on genotype probabilities, and the regression coefficients are random effects.

Last updated 11 months ago

4.04 score 11 stars 6 scripts

polyBreedR - Genomics-assisted breeding for polyploids (and diploids)

Genomics-assisted breeding for polyploids (and diploids)

Last updated 2 months ago

3.78 score 10 stars 6 scripts

GWASpoly - Genome-wide Association Studies for Autopolyploids

Designed for genome-wide association studies in autopolyploids.

Last updated 1 months ago

3.65 score 26 stars 34 scripts

polymapR - Linkage Analysis in Outcrossing Polyploids

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. (2021) <doi:10.1007/s00122-021-03834-x>.

Last updated 6 months ago

3.51 score 1 stars 54 scripts 751 downloads

polyqtlR - QTL Analysis in Autopolyploid Bi-Parental F1 Populations

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>.

Last updated 11 months ago

2.30 score 2 scripts 272 downloads

PolyHaplotyper - Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

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).

Last updated 3 years ago

2.00 score 3 scripts 165 downloads

fitPoly - Genotype Calling for Bi-Allelic Marker Assays

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>.

Last updated 7 years ago

1.00 score 8 scripts 132 downloads