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 5 months ago
polyploidpolyploid-genetic-mappingpolyploidy
23 stars 2.81 score 167 dependencies 1 dependents![](https://github.com/lvclark/polyRAD/raw/HEAD/man/figures/logo.png)
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 7 months ago
bioinformaticsdna-sequencinggenotype-likelihoodsgenotyping-by-sequencinghacktoberfestrad-seqrad-sequencingsnp-genotyping
24 stars 2.71 score 7 dependenciesGWASpoly - Genome-wide Association Studies for Autopolyploids
Designed for genome-wide association studies in autopolyploids.
Last updated 1 years ago
25 stars 2.05 score 39 dependenciesqtlpoly - 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 4 months ago
polyploidqtl-mapping
5 stars 1.86 score 174 dependenciespolyBreedR - Genomics-assisted breeding for polyploids (and diploids)
Genomics-assisted breeding for polyploids (and diploids)
Last updated 1 months ago
8 stars 1.75 score 70 dependenciesdiaQTL - 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 7 months ago
10 stars 1.31 score 56 dependenciespolyqtlR - 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 7 months ago
0.09 score 74 dependenciesPolyHaplotyper - 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
0.00 score 1 dependencies