├── README.md ├── analyses ├── BAC │ ├── .ipynb_checkpoints │ │ ├── TFBSBenchmark-checkpoint.R │ │ ├── Untitled-checkpoint.ipynb │ │ ├── biasCorrectionBenchmark-checkpoint.R │ │ ├── dispersionModel-Copy1-checkpoint.ipynb │ │ ├── dispersionModel-checkpoint.ipynb │ │ ├── footprintingBenchmark-checkpoint.R │ │ ├── getBackgroundDispersion-checkpoint.R │ │ ├── getObservedBias-checkpoint.R │ │ ├── modelInterpretation-checkpoint.ipynb │ │ ├── nucleosomePred-checkpoint.R │ │ └── simulatedFootprints-checkpoint.R │ ├── biasCorrectionBenchmark.R │ ├── dispersionModel.ipynb │ ├── footprintingBenchmark.R │ ├── getBackgroundDispersion.R │ ├── getObservedBias.R │ └── simulatedFootprints.R ├── BMMC │ ├── .ipynb_checkpoints │ │ ├── Fig3_BMMC-checkpoint.ipynb │ │ ├── QC-checkpoint.R │ │ ├── RNACorr-checkpoint.R │ │ ├── TFDynamics-checkpoint.R │ │ ├── TFDynamics-checkpoint.ipynb │ │ ├── cell_type_annotation-checkpoint.ipynb │ │ ├── main-checkpoint.R │ │ ├── nucleosomeTracking-checkpoint.R │ │ ├── plotting-checkpoint.R │ │ ├── preprocessing-checkpoint.R │ │ ├── subCREDynamics-checkpoint.R │ │ ├── test-checkpoint.ipynb │ │ └── test_2-checkpoint.ipynb │ ├── BMMC_CRE_complexity.ipynb │ ├── Fig3_BMMC.ipynb │ ├── QC.R │ ├── cell_type_annotation.ipynb │ ├── main.R │ ├── nucleosomeTracking.R │ ├── plotting.R │ ├── preprocessing.R │ └── scprinter_seq_BMMC_all.ipynb ├── BMMCDonorCellType │ ├── .ipynb_checkpoints │ │ ├── HBB-checkpoint.R │ │ ├── footprintQTL-checkpoint.ipynb │ │ └── main-checkpoint.R │ ├── HBB.R │ ├── main.R │ └── preprocessing.R ├── BMMCTutorial │ ├── .ipynb_checkpoints │ │ ├── BMMCVignette-checkpoint.Rmd │ │ ├── BMMCVignette-checkpoint.pdf │ │ ├── BMMCVignettePrepData-checkpoint.R │ │ └── Untitled-checkpoint.ipynb │ ├── BMMCVignette.Rmd │ ├── BMMCVignette.pdf │ └── BMMCVignettePrepData.R ├── GM12878 │ ├── .ipynb_checkpoints │ │ ├── MNaseComparison-checkpoint.R │ │ ├── QC-checkpoint.R │ │ └── multiScale-checkpoint.R │ ├── MNaseComparison.R │ ├── QC.R │ ├── footprintLoop.sh │ ├── main.R │ ├── multiScale.R │ ├── runFootprinting.sh │ └── runTFBS.sh ├── HepG2 │ ├── .ipynb_checkpoints │ │ ├── Fig2_HepG2-checkpoint.ipynb │ │ ├── QC-checkpoint.R │ │ ├── VplotComparison-checkpoint.R │ │ ├── integratedTracks-checkpoint.R │ │ ├── motifBias-checkpoint.R │ │ ├── plotModels-checkpoint.R │ │ ├── runTOBIAS-checkpoint.sh │ │ ├── signalBleedThrough-checkpoint.R │ │ └── test-checkpoint.ipynb │ ├── Fig2_HepG2.ipynb │ ├── HepG2_delta_clustermap.ipynb │ ├── QC.R │ ├── README.md │ ├── VplotComparison.R │ ├── footprintLoop.sh │ ├── integratedTracks.R │ ├── main.R │ ├── multiScale.R │ ├── runFootprinting.sh │ ├── runTOBIAS.sh │ └── seq2print_HepG2_downsample.ipynb ├── IFNStim │ ├── .ipynb_checkpoints │ │ ├── diffFootprint-checkpoint.R │ │ └── pipeline-checkpoint.sh │ ├── pipeline.sh │ └── scPrinter_IFNG.ipynb ├── K562 │ ├── .ipynb_checkpoints │ │ ├── CRISPRaValidation-checkpoint.R │ │ ├── MNaseComparison-checkpoint.R │ │ ├── QC-checkpoint.R │ │ └── TFTargets-checkpoint.R │ ├── MNaseComparison.R │ ├── QC.R │ ├── footprintLoop.sh │ ├── main.R │ ├── multiScale.R │ ├── runFootprinting.sh │ └── runTFBS.sh ├── PBMCTutorial │ ├── PBMC_bulkATAC_tutorial.ipynb │ └── PBMC_scATAC_tutorial.ipynb ├── TFBSPrediction │ ├── .ipynb_checkpoints │ │ ├── AblationTest-checkpoint.ipynb │ │ ├── AblationTestAllTFs-checkpoint.ipynb │ │ ├── ChIPExoValidation-checkpoint.R │ │ ├── ChIPExoValidation-checkpoint.ipynb │ │ ├── ChIPValidationBMMC-checkpoint.R │ │ ├── ChIPValidationCellLines-checkpoint.R │ │ ├── TFBSPrediction-Copy1-checkpoint.ipynb │ │ ├── TFBSPrediction-checkpoint.ipynb │ │ ├── TFBSPredictionAllTFs-checkpoint.ipynb │ │ ├── TFBSPredictionClusterITFs-checkpoint.ipynb │ │ ├── TFBSTrainingData-checkpoint.R │ │ ├── TFClustering-checkpoint.R │ │ ├── TFModelII-Copy1-checkpoint.ipynb │ │ ├── TFModelII-checkpoint.ipynb │ │ ├── benchmarking-checkpoint.R │ │ ├── featureContribution-checkpoint.ipynb │ │ ├── getDNaseFootprints-checkpoint.R │ │ ├── getJASAPR-checkpoint.R │ │ ├── getMEME-checkpoint.R │ │ ├── modelInterpretation-checkpoint.R │ │ └── modelInterpretation-checkpoint.ipynb │ ├── ChIPExoValidation.R │ ├── README.md │ ├── TFBSTrainingData.R │ ├── TFBS_finetune.ipynb │ ├── TFClustering.R │ ├── benchmarking.R │ ├── footprint_to_TF.ipynb │ ├── getDNaseFootprints.R │ ├── getJASAPR.R │ ├── getMEME.R │ └── unibind │ │ ├── .ipynb_checkpoints │ │ └── getUnibindData-checkpoint.R │ │ └── getUnibindData.R ├── degron │ ├── .ipynb_checkpoints │ │ └── ENCODE_CTCF_degron-checkpoint.ipynb │ └── ENCODE_CTCF_degron.ipynb ├── humanGenomicDNA │ ├── .ipynb_checkpoints │ │ └── getObservedBias-checkpoint.R │ ├── gelSimulation.R │ ├── getObservedBias.R │ └── pipeline.sh ├── inVitroFootprints │ ├── .ipynb_checkpoints │ │ ├── 240607.tobias_invitro_rerun-checkpoint.html │ │ ├── BACSelection-checkpoint.R │ │ ├── Untitled-checkpoint.ipynb │ │ ├── args-checkpoint.txt │ │ ├── benchmark-checkpoint.R │ │ ├── benchmark_boxplots-checkpoint.ipynb │ │ ├── inVitroFootprints-checkpoint.R │ │ └── inVitroFootprints-checkpoint.ipynb │ ├── 240607.tobias_invitro_rerun.html │ ├── BACSelection.R │ ├── benchmark_boxplots.ipynb │ ├── inVitroFootprints.R │ └── inVitroFootprints.ipynb ├── mESC │ ├── .ipynb_checkpoints │ │ └── QC-checkpoint.R │ ├── QC.R │ ├── main.R │ └── multiScale.R ├── mHSCAging10xMultiome │ ├── .RData │ ├── .Rhistory │ ├── .ipynb_checkpoints │ │ ├── ER_stress_validation-checkpoint.ipynb │ │ ├── ER_stress_validation_R-checkpoint.ipynb │ │ ├── Fig4_aging_TF-checkpoint.ipynb │ │ ├── Fig4_mouse_HSC-checkpoint.ipynb │ │ ├── HSCStates-checkpoint.R │ │ ├── HSCStates-checkpoint.ipynb │ │ ├── QC-checkpoint.R │ │ ├── QC-checkpoint.ipynb │ │ ├── TFTargets-checkpoint.R │ │ ├── TFTargets-checkpoint.ipynb │ │ ├── TFTargets_motif_accessibility-checkpoint.ipynb │ │ ├── TFTargets_motif_only-checkpoint.ipynb │ │ ├── TFTargets_relocation-checkpoint.ipynb │ │ ├── Yy1_KO_Bcell-checkpoint.ipynb │ │ ├── Yy1_KO_HSC-Copy2-checkpoint.ipynb │ │ ├── Yy1_KO_HSC-checkpoint.ipynb │ │ ├── aging_TFs-checkpoint.ipynb │ │ ├── cCRE_reorganization-checkpoint.ipynb │ │ ├── cCRE_reorganization_TF_enrichment-checkpoint.ipynb │ │ ├── de_novo_composite_motifs-checkpoint.ipynb │ │ ├── diffAccessibility-checkpoint.R │ │ ├── diffAttribution-checkpoint.R │ │ ├── diffMotifScores-checkpoint.R │ │ ├── diffRNA-checkpoint.R │ │ ├── diffSubCRE-checkpoint.R │ │ ├── diffTFs-checkpoint.R │ │ ├── differential_nucleosome-checkpoint.ipynb │ │ ├── differential_nucleosome_LoRA-checkpoint.ipynb │ │ ├── differential_nucleosome_LoRA_copy-checkpoint.ipynb │ │ ├── differential_nucleosome_TF_ablation-checkpoint.ipynb │ │ ├── differential_nucleosome_TF_enrichment-checkpoint.ipynb │ │ ├── doubletScoring-checkpoint.R │ │ ├── exampleCREs-checkpoint.R │ │ ├── preprocessing-checkpoint.R │ │ ├── pseudobulking-checkpoint.R │ │ ├── runSpectra-checkpoint.ipynb │ │ ├── runSpectra-checkpoint.py │ │ ├── test-checkpoint.ipynb │ │ ├── test-checkpoint.txt │ │ ├── visualization-checkpoint.R │ │ └── visualization-checkpoint.ipynb │ ├── .png │ ├── HSCStates.R │ ├── QC.R │ ├── SEACells │ │ ├── .ipynb_checkpoints │ │ │ ├── SEACells-checkpoint.R │ │ │ └── SEACells-checkpoint.ipynb │ │ ├── SEACells.R │ │ └── SEACells.ipynb │ ├── aging_TFs.ipynb │ ├── de_novo_composite_motifs.ipynb │ ├── diffAccessibility.R │ ├── diffMotifScores.R │ ├── diffRNA.R │ ├── differential_nucleosome.ipynb │ ├── differential_nucleosome_LoRA.ipynb │ ├── differential_nucleosome_TF_ablation.ipynb │ ├── differential_nucleosome_TF_enrichment.ipynb │ ├── doubletScoring.R │ ├── mouseHSC_chromvar.ipynb │ ├── preprocessing.R │ ├── pseudobulking.R │ ├── runSpectra.py │ └── visualization.R ├── refGenomeTn5Bias │ ├── .ipynb_checkpoints │ │ ├── getGenomeTn5Bias-checkpoint.py │ │ ├── runTn5BiasPrediction-checkpoint.sh │ │ └── tmp-checkpoint.py │ ├── getGenomeTn5Bias.py │ └── runTn5BiasPrediction.sh ├── saturatedMut │ ├── BMMC │ │ ├── .ipynb_checkpoints │ │ │ └── main-checkpoint.R │ │ └── main.R │ └── HepG2 │ │ ├── .ipynb_checkpoints │ │ └── main-checkpoint.R │ │ └── main.R ├── sequenceModels │ ├── TF_clustering │ │ ├── .ipynb_checkpoints │ │ │ └── TF_clustering-checkpoint.ipynb │ │ └── TF_clustering.ipynb │ ├── chromBPNet │ │ ├── .ipynb_checkpoints │ │ │ ├── chromBPNetBenchmark-checkpoint.R │ │ │ ├── chromBPNetComparison-checkpoint.R │ │ │ └── chromBPNetGenomicDNABias-checkpoint.R │ │ ├── chromBPNetComparison.R │ │ └── chromBPNetGenomicDNABias.R │ ├── scPrinter │ │ └── prediction │ │ │ ├── .ipynb_checkpoints │ │ │ ├── benchmarking-checkpoint.R │ │ │ └── getChIPTFBS-checkpoint.R │ │ │ ├── benchmarking.R │ │ │ └── getChIPTFBS.R │ └── variants │ │ ├── .ipynb_checkpoints │ │ ├── MPRA_Kircher_et_al_2019-checkpoint.R │ │ └── fine_mapped_variants_Ulirsch_et_al_2019-checkpoint.R │ │ └── MPRA_Kircher_et_al_2019.R └── yeast │ ├── .ipynb_checkpoints │ ├── Untitled-checkpoint.ipynb │ ├── nucPrediction-checkpoint.R │ ├── nucPrediction-checkpoint.ipynb │ ├── nucTrainingData-checkpoint.R │ └── preprocessing-checkpoint.R │ ├── ATACPipeline.sh │ ├── footprintLoop.sh │ ├── main.R │ ├── nucPrediction.R │ ├── nucPrediction.ipynb │ ├── nucTrainingData.R │ ├── nucleoATAC.sh │ ├── preprocessing.R │ └── runFootprinting.sh ├── code ├── .ipynb_checkpoints │ ├── filterFrags-checkpoint.R │ ├── filterPeaks-checkpoint.R │ ├── getFootprints-checkpoint.R │ ├── getGeneCorr-checkpoint.R │ ├── getGroupData-checkpoint.R │ ├── getTargetPathway-checkpoint.R │ ├── liftOverFrags-checkpoint.R │ ├── requirements-checkpoint.txt │ └── utils-checkpoint.R ├── Palantir.py ├── filterFrags.R ├── filterPeaks.R ├── footprintTracking.R ├── getAggregateFootprint.R ├── getBias.R ├── getCounts.R ├── getFootprints.R ├── getGeneCorr.R ├── getGroupData.R ├── getModelPrediction.R ├── getPseudoBulks.R ├── getSubstructures.R ├── getTFBS.R ├── getTargetPathway.R ├── liftOverFrags.R ├── predictBias.py ├── renameRead.py ├── utils.R └── visualization.R └── data ├── BAC ├── BACs.bed └── Tn5PWM.rds ├── BMMCTutorial ├── BMMCTutorialFragments.tsv ├── BMMCTutorialRegions.bed ├── barcodeGrouping.txt.gz ├── groupInfo.txt └── predBias.rds ├── GM12878 └── pipeline.sh ├── HepG2 └── pipeline.sh ├── K562 └── pipeline.sh ├── mHSCAging10xMultiome ├── hemeMarkers.txt └── pipeline.sh └── shared ├── BlacklistFiles ├── hg19.full.blacklist.bed ├── hg19_blacklist.JDB.bed ├── hg38-blacklist.v2.bed ├── mm10.full.blacklist.bed ├── mm10_blacklist.JDB.bed └── mm9_blacklist.JDB.bed ├── TFTypes.txt ├── Tn5ModelTutorial.ipynb ├── Tn5_NN_model.h5 ├── cisBP_human_pwms_2021.rds ├── cisBP_mouse_pwms_2021.rds ├── dispModel ├── dispersionModel100bp.h5 ├── dispersionModel100bp.rds ├── dispersionModel10bp.h5 ├── dispersionModel10bp.rds ├── dispersionModel11bp.h5 ├── dispersionModel11bp.rds ├── dispersionModel12bp.h5 ├── dispersionModel12bp.rds ├── dispersionModel13bp.h5 ├── dispersionModel13bp.rds ├── dispersionModel14bp.h5 ├── dispersionModel14bp.rds ├── dispersionModel15bp.h5 ├── dispersionModel15bp.rds ├── dispersionModel16bp.h5 ├── dispersionModel16bp.rds ├── dispersionModel17bp.h5 ├── dispersionModel17bp.rds ├── dispersionModel18bp.h5 ├── dispersionModel18bp.rds ├── dispersionModel19bp.h5 ├── dispersionModel19bp.rds ├── dispersionModel20bp.h5 ├── dispersionModel20bp.rds ├── dispersionModel21bp.h5 ├── dispersionModel21bp.rds ├── dispersionModel22bp.h5 ├── dispersionModel22bp.rds ├── dispersionModel23bp.h5 ├── dispersionModel23bp.rds ├── dispersionModel24bp.h5 ├── dispersionModel24bp.rds ├── dispersionModel25bp.h5 ├── dispersionModel25bp.rds ├── dispersionModel26bp.h5 ├── dispersionModel26bp.rds ├── dispersionModel27bp.h5 ├── dispersionModel27bp.rds ├── dispersionModel28bp.h5 ├── dispersionModel28bp.rds ├── dispersionModel29bp.h5 ├── dispersionModel29bp.rds ├── dispersionModel2bp.h5 ├── dispersionModel2bp.rds ├── dispersionModel30bp.h5 ├── dispersionModel30bp.rds ├── dispersionModel31bp.h5 ├── dispersionModel31bp.rds ├── dispersionModel32bp.h5 ├── dispersionModel32bp.rds ├── dispersionModel33bp.h5 ├── dispersionModel33bp.rds ├── dispersionModel34bp.h5 ├── dispersionModel34bp.rds ├── dispersionModel35bp.h5 ├── dispersionModel35bp.rds ├── dispersionModel36bp.h5 ├── dispersionModel36bp.rds ├── dispersionModel37bp.h5 ├── dispersionModel37bp.rds ├── dispersionModel38bp.h5 ├── dispersionModel38bp.rds ├── dispersionModel39bp.h5 ├── dispersionModel39bp.rds ├── dispersionModel3bp.h5 ├── dispersionModel3bp.rds ├── dispersionModel40bp.h5 ├── dispersionModel40bp.rds ├── dispersionModel41bp.h5 ├── dispersionModel41bp.rds ├── dispersionModel42bp.h5 ├── dispersionModel42bp.rds ├── dispersionModel43bp.h5 ├── dispersionModel43bp.rds ├── dispersionModel44bp.h5 ├── dispersionModel44bp.rds ├── dispersionModel45bp.h5 ├── dispersionModel45bp.rds ├── dispersionModel46bp.h5 ├── dispersionModel46bp.rds ├── dispersionModel47bp.h5 ├── dispersionModel47bp.rds ├── dispersionModel48bp.h5 ├── dispersionModel48bp.rds ├── dispersionModel49bp.h5 ├── dispersionModel49bp.rds ├── dispersionModel4bp.h5 ├── dispersionModel4bp.rds ├── dispersionModel50bp.h5 ├── dispersionModel50bp.rds ├── dispersionModel51bp.h5 ├── dispersionModel51bp.rds ├── dispersionModel52bp.h5 ├── dispersionModel52bp.rds ├── dispersionModel53bp.h5 ├── dispersionModel53bp.rds ├── dispersionModel54bp.h5 ├── dispersionModel54bp.rds ├── dispersionModel55bp.h5 ├── dispersionModel55bp.rds ├── dispersionModel56bp.h5 ├── dispersionModel56bp.rds ├── dispersionModel57bp.h5 ├── dispersionModel57bp.rds ├── dispersionModel58bp.h5 ├── dispersionModel58bp.rds ├── dispersionModel59bp.h5 ├── dispersionModel59bp.rds ├── dispersionModel5bp.h5 ├── dispersionModel5bp.rds ├── dispersionModel60bp.h5 ├── dispersionModel60bp.rds ├── dispersionModel61bp.h5 ├── dispersionModel61bp.rds ├── dispersionModel62bp.h5 ├── dispersionModel62bp.rds ├── dispersionModel63bp.h5 ├── dispersionModel63bp.rds ├── dispersionModel64bp.h5 ├── dispersionModel64bp.rds ├── dispersionModel65bp.h5 ├── dispersionModel65bp.rds ├── dispersionModel66bp.h5 ├── dispersionModel66bp.rds ├── dispersionModel67bp.h5 ├── dispersionModel67bp.rds ├── dispersionModel68bp.h5 ├── dispersionModel68bp.rds ├── dispersionModel69bp.h5 ├── dispersionModel69bp.rds ├── dispersionModel6bp.h5 ├── dispersionModel6bp.rds ├── dispersionModel70bp.h5 ├── dispersionModel70bp.rds ├── dispersionModel71bp.h5 ├── dispersionModel71bp.rds ├── dispersionModel72bp.h5 ├── dispersionModel72bp.rds ├── dispersionModel73bp.h5 ├── dispersionModel73bp.rds ├── dispersionModel74bp.h5 ├── dispersionModel74bp.rds ├── dispersionModel75bp.h5 ├── dispersionModel75bp.rds ├── dispersionModel76bp.h5 ├── dispersionModel76bp.rds ├── dispersionModel77bp.h5 ├── dispersionModel77bp.rds ├── dispersionModel78bp.h5 ├── dispersionModel78bp.rds ├── dispersionModel79bp.h5 ├── dispersionModel79bp.rds ├── dispersionModel7bp.h5 ├── dispersionModel7bp.rds ├── dispersionModel80bp.h5 ├── dispersionModel80bp.rds ├── dispersionModel81bp.h5 ├── dispersionModel81bp.rds ├── dispersionModel82bp.h5 ├── dispersionModel82bp.rds ├── dispersionModel83bp.h5 ├── dispersionModel83bp.rds ├── dispersionModel84bp.h5 ├── dispersionModel84bp.rds ├── dispersionModel85bp.h5 ├── dispersionModel85bp.rds ├── dispersionModel86bp.h5 ├── dispersionModel86bp.rds ├── dispersionModel87bp.h5 ├── dispersionModel87bp.rds ├── dispersionModel88bp.h5 ├── dispersionModel88bp.rds ├── dispersionModel89bp.h5 ├── dispersionModel89bp.rds ├── dispersionModel8bp.h5 ├── dispersionModel8bp.rds ├── dispersionModel90bp.h5 ├── dispersionModel90bp.rds ├── dispersionModel91bp.h5 ├── dispersionModel91bp.rds ├── dispersionModel92bp.h5 ├── dispersionModel92bp.rds ├── dispersionModel93bp.h5 ├── dispersionModel93bp.rds ├── dispersionModel94bp.h5 ├── dispersionModel94bp.rds ├── dispersionModel95bp.h5 ├── dispersionModel95bp.rds ├── dispersionModel96bp.h5 ├── dispersionModel96bp.rds ├── dispersionModel97bp.h5 ├── dispersionModel97bp.rds ├── dispersionModel98bp.h5 ├── 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