├── .Rhistory ├── .gitignore ├── LICENSE.txt ├── Makefile ├── README.md ├── SampleSheet.csv ├── annotation ├── chrom_hg19.sizes ├── chrom_hg38.sizes ├── chrom_mm10.sizes ├── hg19_blacklist.bed ├── hg19_enhancer.bed ├── hg19_promoter.bed ├── hg19_tss.bed ├── hg38_blacklist.bed ├── hg38_enhancer.bed ├── hg38_promoter.bed ├── hg38_tss.bed ├── mm10_blacklist.bed ├── mm10_enhancer.bed ├── mm10_promoter.bed └── mm10_tss.bed ├── complete_update_history.md ├── configure_system.txt ├── configure_user.txt ├── doc ├── AccessQCInR.html ├── AccessResultsInR.html ├── _site │ ├── Downstream_in_R.html │ ├── Downstream_in_R_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── QC_in_R.html │ ├── QC_in_R_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── Redo_Downstream_in_R.html │ ├── Redo_Downstream_in_R_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-4-1.png │ ├── about.html │ ├── index.html │ ├── site_libs │ │ ├── bootstrap-3.3.5 │ │ │ ├── css │ │ │ │ ├── bootstrap-theme.css │ │ │ │ ├── bootstrap-theme.css.map │ │ │ │ ├── bootstrap-theme.min.css │ │ │ │ ├── bootstrap.css │ │ │ │ ├── bootstrap.css.map │ │ │ │ ├── bootstrap.min.css │ │ │ │ ├── cerulean.min.css │ │ │ │ ├── cosmo.min.css │ │ │ │ ├── darkly.min.css │ │ │ │ ├── flatly.min.css │ │ │ │ ├── fonts │ │ │ │ │ ├── Lato.ttf │ │ │ │ │ ├── LatoBold.ttf │ │ │ │ │ ├── LatoItalic.ttf │ │ │ │ │ ├── NewsCycle.ttf │ │ │ │ │ ├── NewsCycleBold.ttf │ │ │ │ │ ├── OpenSans.ttf │ │ │ │ │ ├── OpenSansBold.ttf │ │ │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ │ │ ├── OpenSansItalic.ttf │ │ │ │ │ ├── OpenSansLight.ttf │ │ │ │ │ ├── OpenSansLightItalic.ttf │ │ │ │ │ ├── Raleway.ttf │ │ │ │ │ ├── RalewayBold.ttf │ │ │ │ │ ├── Roboto.ttf │ │ │ │ │ ├── RobotoBold.ttf │ │ │ │ │ ├── RobotoLight.ttf │ │ │ │ │ ├── RobotoMedium.ttf │ │ │ │ │ ├── SourceSansPro.ttf │ │ │ │ │ ├── SourceSansProBold.ttf │ │ │ │ │ ├── SourceSansProItalic.ttf │ │ │ │ │ ├── SourceSansProLight.ttf │ │ │ │ │ └── Ubuntu.ttf │ │ │ │ ├── journal.min.css │ │ │ │ ├── lumen.min.css │ │ │ │ ├── paper.min.css │ │ │ │ ├── readable.min.css │ │ │ │ ├── sandstone.min.css │ │ │ │ ├── simplex.min.css │ │ │ │ ├── spacelab.min.css │ │ │ │ ├── united.min.css │ │ │ │ └── yeti.min.css │ │ │ ├── fonts │ │ │ │ ├── glyphicons-halflings-regular.eot │ │ │ │ ├── glyphicons-halflings-regular.svg │ │ │ │ ├── glyphicons-halflings-regular.ttf │ │ │ │ ├── glyphicons-halflings-regular.woff │ │ │ │ └── glyphicons-halflings-regular.woff2 │ │ │ ├── js │ │ │ │ ├── bootstrap.js │ │ │ │ ├── bootstrap.min.js │ │ │ │ └── npm.js │ │ │ └── shim │ │ │ │ ├── html5shiv.min.js │ │ │ │ └── respond.min.js │ │ ├── header-attrs-2.1 │ │ │ └── header-attrs.js │ │ ├── jquery-1.11.3 │ │ │ └── jquery.min.js │ │ ├── jqueryui-1.11.4 │ │ │ ├── README │ │ │ ├── images │ │ │ │ ├── ui-icons_444444_256x240.png │ │ │ │ ├── ui-icons_555555_256x240.png │ │ │ │ ├── ui-icons_777620_256x240.png │ │ │ │ ├── ui-icons_777777_256x240.png │ │ │ │ ├── ui-icons_cc0000_256x240.png │ │ │ │ └── ui-icons_ffffff_256x240.png │ │ │ ├── index.html │ │ │ ├── jquery-ui.css │ │ │ ├── jquery-ui.js │ │ │ ├── jquery-ui.min.css │ │ │ ├── jquery-ui.min.js │ │ │ ├── jquery-ui.structure.css │ │ │ ├── jquery-ui.structure.min.css │ │ │ ├── jquery-ui.theme.css │ │ │ └── jquery-ui.theme.min.css │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ ├── navigation-1.1 │ │ │ ├── codefolding.js │ │ │ ├── sourceembed.js │ │ │ └── tabsets.js │ │ └── tocify-1.9.1 │ │ │ ├── jquery.tocify.css │ │ │ └── jquery.tocify.js │ └── style.css └── fig1.png ├── scATAC-pro └── scripts ├── .Rhistory ├── Makefile ├── addCB2bam.sh ├── all.sh ├── bam2qc.sh ├── call_cell.sh ├── call_peak.sh ├── cell_mapping_qc.sh ├── clustering.sh ├── convert10xbam.sh ├── convert10xbam_short.sh ├── dex_fastq.sh ├── dex_fastq_single.sh ├── downstream.sh ├── footprint.sh ├── footprint_by_cluster.sh ├── generate_signal.sh ├── get_bam4Cells.sh ├── get_mtx.sh ├── install ├── Makefile ├── install_Rpackages.R └── install_dependencies.sh ├── integrate.sh ├── integrate_csv.sh ├── integrate_mtx.sh ├── integrate_peak.sh ├── iter_peak.sh ├── labelTransfer.sh ├── mapping.sh ├── mapping_bowtie.sh ├── mapping_bowtie2.sh ├── mapping_bwa.sh ├── mapping_qc.sh ├── mergePeaks.sh ├── motif_analysis.sh ├── process.sh ├── process_from_align.sh ├── process_no_dex.sh ├── process_with_bam.sh ├── qc_per_barcode.sh ├── reConstMtx.sh ├── read_conf.sh ├── report.sh ├── report_dynamic.sh ├── reprocess_cellranger_output.sh ├── rmDoublets.sh ├── runCicero.sh ├── runDA.sh ├── runGO.sh ├── split_bam2clusters.sh ├── src ├── .Rhistory ├── EmptyDrop.R ├── bc_corr4frags.R ├── cellranger_cell_caller.R ├── clustering.R ├── dex_fastq.py ├── dex_fastq_extraIndex.py ├── dsAnalysis_utilities.R ├── extendPeaks.R ├── extract_bam4Cells.pl ├── extract_bam4Cells_old.pl ├── filter_barcodes.R ├── filter_frags.R ├── generate_gene_cisActivity.R ├── get_mtx.R ├── get_qc_per_barcode.R ├── integrate_mtx.R ├── integrate_mtx_csv.R ├── interface2cello.R ├── labelTransfer.R ├── launch_viscello.R ├── mergePeaks.R ├── mergePeaks_csv.R ├── merge_peaks_cls.R ├── motif_analysis.R ├── reConstMtx.R ├── render2report.R ├── render2report_dynamic.R ├── rmDoublets.R ├── rmRedundantPeaks.R ├── rm_minor_cluster.R ├── runCicero.R ├── runDA.R ├── runGO.R ├── run_zinba.R ├── scATAC-pro_report.Rmd ├── scATAC-pro_report_dynamic.Rmd ├── scATAC-pro_utils.R ├── simply_bam2frags.pl ├── simply_bam2frags_singleEnd.pl ├── sort_frags.R ├── split_bam2clusters.pl ├── split_bam2clusters0.pl └── 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