Qploidy2

Qploidy2 is an R package designed for large-scale copy number variation, ploidy and aneuploidy estimation using genotyping platforms data.

Qploidy2 builds upon the original Qploidy package. While Qploidy focused on signal standardization to reduce noise for ploidy estimation and relied heavily on visual inspection of diagnostic plots, Qploidy2 introduces a multipoint approach using a Hidden Markov Model (HMM). This advanced method combines information from standardized allele ratios and total depth/intensities to provide automated and robust copy number estimation.