├── .DS_Store ├── .Rbuildignore ├── .Rprofile ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── mirror.yml │ └── pkgdown.yaml ├── .gitignore ├── .renvignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── PICsnATAC.Rproj ├── R ├── .DS_Store ├── Insertion_rates_and_DAR_test.R ├── PIC_function.R └── param_estimate_joint_p_q.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── analysis_codes ├── .DS_Store ├── 10X_data_insertion_vs_fragment_check.R ├── 10X_data_insertion_vs_fragment_check_additional_bin_matrix.R ├── 10X_data_insertion_vs_fragment_check_bin_matrix_generation.R ├── Modeling__apply_to_PBMC_data.R ├── P0_kidney_signac_counting.R ├── PBMC_data__DAR_comparison_PIC_model_local_MLE_fc_filtered.R ├── PBMC_multiome_sorted__DAR_comparison_PIC_vs_binary_ArchR_vs_Seurat.R ├── archR_signac_counting.R ├── cicero_analysis_with_pbmc_data.R ├── kidney_data__DAR_comparison_comb.R ├── kidney_data__estimate_the_open_probability_new_insertion_fragment.R ├── open_prob_correlations_human_cell_line_data.R ├── other_methods_for_differential_cleaned.R ├── simulation_insertion_frag_Pois.R ├── summarize_10K_sorted_1.R └── summarize_10K_sorted_2.R ├── inst └── CITATION ├── man ├── DAR_by_LRT.Rd ├── PIC_counting.Rd ├── count_peaks.Rd ├── data_frame_to_GRanges.Rd ├── figures │ ├── README-F1a.pdf │ ├── README-F1a.png │ ├── README-F1a.svg │ ├── README-F1c.heic │ ├── README-F1c.pdf │ ├── README-F1c.svg │ ├── README-F1d.heic │ ├── README-F1d.pdf │ └── README-F1d.svg ├── get_r_by_ct_mat_pq.Rd ├── load_fragments.Rd ├── obs_to_insertion_ME.Rd ├── obs_to_insertion_MLE_lam.Rd └── obs_to_insertion_MLE_obj.Rd ├── renv.lock ├── renv ├── .gitignore ├── activate.R ├── settings.dcf └── settings.json ├── tests ├── testthat.R └── testthat │ ├── data │ ├── atac_fragment_test.tsv.gz │ ├── atac_pbmc_5k_nextgem_peaks.bed │ ├── atac_singlecell_test_sub.csv │ └── output.tsv.gz │ └── test-PIC_counting.R └── vignettes ├── .DS_Store ├── 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