R-universe - cristianetaniguti (Cris Taniguti)

onemap - Construction of Genetic Maps in Experimental Crosses

Analysis of molecular marker data from model and non-model systems. For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu and colleagues (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multi-point approaches using hidden Markov models.

Last updated

cpp

8.08 score 5 stars 172 scripts 795 downloads

Qploidy - Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Provides functions for estimating ploidy levels and detecting aneuploidy in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements method described in Taniguti et al. (2025) <doi:10.1002/tpg2.70044> an extended version of the 'PennCNV' signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.

Last updated

5.30 score 5 stars 6 scripts 251 downloads