How to Cite | References

When does the Qploidy methodology work? | When does the Qploidy methodology NOT work? | Installation | Input files | Target sequencing VCF file | From Axiom array summary file | From Illumina array | Define Reference Samples - Choose Path (1) or (2) | (1) Using a Subset with Known Ploidy | (2) Using the Most Common Ploidy | (1) and (2) Run Dosage Caller | Target sequencing VCF data | (1) Filter the genos object to keep only the known ploidy samples subset | Array data | (1) and (2) Standardization | Recover the ploidy_standardization Object from a Saved File | (1) and (2) Plot results | (1) and (2) Ploidy Estimation for All Samples | Export ploidy result table | (1) and (2) Save plots for all samples | (2) Improve standardization selecting a known ploidy subset after first round | HMM-based Copy Number Estimation and Visualization | HMM-based Copy Number Estimation | Parallel HMM Estimation for Multiple Samples | Summarizing Parallel HMM Results | Interpreting the CN Track Plot | Try the Qploidy Shiny App! | How to cite | Acknowledgments | Version 1.0.0 | Versions > 1.0.0

Getting started | Functions | Getting help | Packages | Importing and exporting data | Classes and methods | Saving your work | References