├── .Rbuildignore ├── CommonProblems.md ├── DESCRIPTION ├── Evaluation ├── method_evaluation.R ├── method_evaluation.Rmd └── method_evaluation.html ├── LICENSE ├── NAMESPACE ├── NEWS ├── R └── MAUDE.R ├── README.md ├── doc ├── BACH2_base_editor_screen.R ├── BACH2_base_editor_screen.html ├── CD69_tutorial.R ├── CD69_tutorial.html ├── simulated_data_tutorial.R └── simulated_data_tutorial.html ├── images └── logo2.png ├── inst ├── CITATION └── extdata │ ├── CD69_bin_percentiles.txt │ └── Encode_Jurkat_DHS_both.merged.bed ├── man ├── calcFDRByExperiment.Rd ├── combineZStouffer.Rd ├── findGuideHits.Rd ├── findGuideHitsAllScreens.Rd ├── findOverlappingElements.Rd ├── getElementwiseStats.Rd ├── getNBGaussianLikelihood.Rd ├── getTilingElementwiseStats.Rd ├── getZScalesWithNTGuides.Rd └── makeBinModel.Rd └── vignettes ├── BACH2_base_editor_screen.Rmd ├── BACH2_data ├── loaded_BACH2_BE_CRISPResso_data.txt.gz └── sample_metadata.txt ├── CD69_tutorial.Rmd └── simulated_data_tutorial.Rmd 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