├── .DS_Store ├── .RData ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── NIPTeR.Rproj ├── R ├── Sample.R ├── best_fit_beta.R ├── bin_gc_correct.R ├── bin_sample.R ├── chi_correction.R ├── constants.R ├── control_group.R ├── diagnose_control_group.R ├── gc_correct.R ├── gc_correct_distribute.R ├── general_functions.R ├── ncv_calculation.R ├── ncv_template.R ├── prepare_ncv_template.R ├── regression.R ├── regression_result.R ├── sysdata.rda └── z_score.R ├── README.Rmd ├── README.md ├── cran-comments.md ├── man ├── add_samples_controlgroup.Rd ├── as_control_group.Rd ├── bin_bam_sample.Rd ├── calculate_ncv_score.Rd ├── calculate_z_score.Rd ├── chi_correct.Rd ├── chrfractions.Rd ├── diagnose_control_group.Rd ├── gc_correct.Rd ├── getcontrolchromosomes.Rd ├── getfractionscontrolgroup.Rd ├── getreadscontrolgroup.Rd ├── match_control_group.Rd ├── perform_regression.Rd ├── prepare_ncv.Rd ├── remove_duplicates_controlgroup.Rd ├── remove_sample_controlgroup.Rd └── retrieve_fractions_of_interest.Rd ├── test_samples ├── NIPTeR_cleaned_87_controls.rds └── Trisomy21.rds └── vignettes ├── .DS_Store ├── NIPTeR.Rmd └── figures ├── .DS_Store ├── complex_workflow.png ├── control_group_workflow.png └── simple_workflow.png /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molgenis/NIPTeR/HEAD/.DS_Store -------------------------------------------------------------------------------- /.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molgenis/NIPTeR/HEAD/.RData -------------------------------------------------------------------------------- /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/molgenis/NIPTeR/HEAD/.Rbuildignore 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