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Merged
Cristianetaniguti merged 1 commit into from
May 20, 2026
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add ref #4

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17 changes: 14 additions & 3 deletions README.md
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Expand Up @@ -39,11 +39,22 @@ If you find a bug or want an enhancement, please submit an issue [here](https://

## How to cite

* `Qploidy` standardization approach
### Qploidy - Standardization

Taniguti, C. H., Lau, J., Hochhaus, T., Arias, D. C. L., Hokanson, S. C., Zlesak, D. C., Byrne, D. H., Klein, P. E., & Riera-Lizarazu, O. (2025). Exploring chromosomal variations in garden roses: Insights from high-density SNP array data and a new tool, Qploidy2. The Plant Genome, e70044. https://doi.org/10.1002/tpg2.70044
Taniguti, C. H., Lau, J., Hochhaus, T., Arias, D. C. L., Hokanson, S. C., Zlesak, D. C., Byrne, D. H.,
Klein, P. E., & Riera-Lizarazu, O. (2025). Exploring chromosomal variations in garden roses: Insights
from high-density SNP array data and a new tool, Qploidy. The Plant Genome, e70044.
https://doi.org/10.1002/tpg2.70044

* `Qploidy2` HMM copy number estimation - manuscript in preparation
### Qploidy2 - HMM and grid approach BAF model selection

Manuscript in preparation. Please contact the author for more information.

### nQuack - EM approach BAF model selection

Gaynor, M., Landis, J., O'Connor, T., Laport, R., Doyle, J., Soltis, D., Ponciano, J., & Soltis, P. (2024).
"nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity."
Applications in Plant Sciences, 12(4), e11606. doi:10.1002/aps3.11606

## Acknowledgments

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6 changes: 6 additions & 0 deletions docs/Qploidy_alfalfa_tutorial.Rmd
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Expand Up @@ -662,6 +662,12 @@ https://doi.org/10.1002/tpg2.70044

Manuscript in preparation. Please contact the author for more information.

### nQuack - BAF model selection

Gaynor, M., Landis, J., O'Connor, T., Laport, R., Doyle, J., Soltis, D., Ponciano, J., & Soltis, P. (2024).
"nQuack: An R package for predicting ploidal level from sequence data using site-based heterozygosity."
Applications in Plant Sciences, 12(4), e11606. doi:10.1002/aps3.11606

# Acknowledgments

### Qploidy version 1.0.0
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