├── .gitattributes ├── .gitignore ├── .idea ├── .gitignore ├── deployment.xml ├── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── misc.xml ├── modules.xml ├── sc_nano_bcd_CUT_Tag.iml ├── sshConfigs.xml ├── vcs.xml └── webServers.xml ├── README.md ├── cicero_ongoing.R ├── config ├── bingren_files.txt ├── bingren_snap_files.txt ├── bingren_snap_fles.txt └── config.yaml ├── demultiplex_condor ├── P232019_1001_L001.submit ├── P232019_1001_L002.submit ├── P232019_1002_L001.submit ├── P232019_1002_L002.submit ├── cellranger_bcdCT_MB21_02.submit └── cellranger_bcdCT_MB21_03.submit ├── env ├── environment_magic.yaml └── environtment.yaml ├── magic_ongoing.R ├── magic_ongoing.Rmd ├── notebooks ├── Adult_ATAC_10x.ipynb ├── Adult_ATAC_10x_analysis.Rmd ├── FrIP_same_peakset.ipynb ├── bcdCT_MB21_02 │ ├── bcdCT_MB21_02.Rmd │ ├── bcdCT_MB21_02_export_bw.Rmd │ ├── bcdCT_MB21_02_integration.Rmd │ └── bcdCT_MB21_02_integration_RNA.Rmd ├── devel │ ├── H3K27ac_H3K27me3 │ │ ├── H3K27ac_H3K27me3.Rmd │ │ └── bcdCT_MB21_02_integration_RNA.Rmd │ ├── allevium_test.Rmd │ ├── bcdCT_MB21_01.Rmd │ ├── bcdCT_MB21_02 │ │ ├── bcdCT_MB21_02.Rmd │ │ ├── bcdCT_MB21_02_export_bw.Rmd │ │ ├── bcdCT_MB21_02_integration.Rmd │ │ └── bcdCT_MB21_02_integration_RNA.Rmd │ ├── cicero.Rmd │ ├── cicero.nb.html │ ├── export_for_scvelo.Rmd │ ├── fraction_in_specific_peaks.Rmd │ ├── merge │ │ └── bcdCT_MB21_02.Rmd │ ├── multimodal │ │ └── WNN_multimodal.RMd │ ├── multiple_modalities │ │ └── ATAC_H3K27ac_H3K27me3 │ │ │ └── rename_clusters.Rmd │ ├── pick_cells_summarize.Rmd │ └── plot_genome_browser.Rmd ├── figures │ ├── figure1.Rmd │ ├── figure2.Rmd │ ├── figure3.Rmd │ ├── figure4.Rmd │ ├── figure5.Rmd │ ├── figure6.Rmd │ ├── plot_genome_browser.Rmd │ ├── revision_benchmark_downscaled.ipynb │ ├── revision_downscale.ipynb │ ├── revision_gopalan_comparison.ipynb │ ├── revision_pt_integration.ipynb │ ├── revision_sc_nano_comparisons.ipynb │ ├── revison_shared_distinct_comparison.ipynb │ └── scvelo_figure6.ipynb ├── merge │ └── bcdCT_MB21_02.Rmd ├── multimodal │ └── WNN_Seurat.Rmd ├── precision_recall_peaks.ipynb ├── single_modality │ ├── ATAC_rename_clusters.Rmd │ ├── H3K27ac_rename_clusters.Rmd │ ├── H3K27me3_rename_clusters.Rmd │ └── H3K4me3_rename_clusters.Rmd └── summary │ └── summary_clustering.Rmd ├── run_pipeline.sh ├── scripts ├── UMAP_cluster.R ├── add_barcode_to_readID.py ├── add_barcode_to_readID_new.py ├── add_meta_module_from_bed_to_seurat.R ├── add_sampleID_to_bam.py ├── add_sample_to_fragments.py ├── add_sample_to_list.py ├── all_bam_to_bw.sh ├── all_bam_to_peaks.sh ├── create_seurat_bingren.R ├── create_seurat_object.R ├── debarcode.py ├── devel │ ├── merge_modalities.R │ └── select_top_regions_from_matrix.R ├── download_10x_scATAC.sh ├── download_encode.sh ├── export_bw.R ├── export_cluster_barcode_table.R ├── filter_bam_by_barcode.py ├── filter_peaks_by_matrix.R ├── find_L3_markers.R ├── find_LA_duplicates_in_bam_faster.py ├── find_markers.R ├── func.R ├── get_cell_barcode.awk ├── integrate_CT_ATAC.R ├── integrate_CT_RNAseq.R ├── markers_to_bed.R ├── matrix_get_specific_regions.R ├── merge_modalities.R ├── merge_modalities2.R ├── merge_objects.R ├── pick_cells.R ├── run_slingshot.R ├── select_top_regions_from_matrix.R ├── seurat_export_h5.R ├── seurat_to_scvelo.R ├── snap_to_seurat.R ├── subset_bingren_scATAC.py └── subset_bingren_scATAC_snap.R └── workflow ├── Snakefile ├── Snakefile_benchmarking.smk ├── Snakefile_downscale.smk ├── Snakefile_figures.smk ├── Snakefile_multiCT.smk ├── Snakefile_multi_CT ├── Snakefile_multi_CT.smk ├── Snakefile_multimodal.smk ├── Snakefile_nbiotech.smk ├── Snakefile_pre_nbiotech.smk ├── Snakefile_precision_recall.smk ├── Snakefile_prep.smk ├── Snakefile_preprocess.smk ├── Snakefile_scATAC.smk ├── Snakefile_single_modality.smk └── devel ├── Snakefile_QC └── Snakefile_figures.smk /.gitattributes: -------------------------------------------------------------------------------- 1 | *.html 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