├── README.md ├── figure1 ├── Denoising AutoEncoder - Evaluation.ipynb ├── Denoising AutoEncoder Nearest Neighbor Analysis.ipynb ├── DenoisingAutoEncoder Training.ipynb ├── IterativeLSI Nearest Neighbor Analysis.ipynb ├── README.md ├── Supplementary Figure2 Code │ ├── .DS_Store │ ├── README.md │ ├── Supplementary_Figure2D_E.R │ ├── Supplementary_figure2A.R │ └── pileup_data │ │ ├── BLCA_manifest.txt │ │ ├── CDKN2A_PANCAN_pileup_part_intron.RData │ │ └── COAD_manifest.txt ├── TCGA Immune Cells Differential to nearest neighbor Code.ipynb ├── TCGA-Computing the 10MB CNV like ATAC signal.ipynb ├── TCGA_Helper.R └── drscax │ ├── create_adata.py │ ├── create_peakrds.R │ ├── create_sparsematrix.R │ ├── data.py │ ├── eval_.py │ ├── models.py │ ├── pancancer_AddPeaks.R │ ├── readme.MD │ └── train.py ├── figure2 ├── README.md ├── TCGA Footprint comparison & plotting.ipynb ├── create_cancerspecific_peaks.R ├── ism_motif_mutation │ ├── README.md │ └── scripts │ │ ├── motifism_aggregate.py │ │ ├── motifism_launch.sh │ │ ├── motifism_score.py │ │ ├── mutationism_aggregate.py │ │ ├── mutationism_launch.sh │ │ ├── mutationism_score.py │ │ ├── regdiffdata.py │ │ └── regdiffmodels.py ├── motif_enrichments │ ├── README.md │ ├── helper_utils.py │ └── motif_enrichment_cmp_plots.ipynb └── training_models │ ├── README.md │ ├── foldtrainer.py │ ├── foldtrainer.sh │ └── launch_training_jobs.py ├── figure3 ├── README.md ├── Subclonal analysis │ ├── README.md │ ├── TCGA Example Analysis.Rmd │ ├── TCGA-06-A5U0-allelic-CN.tsv │ ├── TCGA-06-A5U0_sce.rds │ ├── TCGA-4W-AA9S-allelic-CN.tsv │ └── TCGA-4W-AA9S_sce.rds ├── Subclonal_Adult_Fetal_like_motif_analysis │ ├── README.md │ ├── gbm_subclone_tf_enrichment_chr6.ipynb │ └── gbm_subclones_adult_fetal_motifs.ipynb └── Subclone related scATAC analysis │ ├── Data │ ├── GBM39_peaks_cnv_annotated.csv │ ├── GBM45_peaks_cnv_annotated.csv │ ├── adult_significant_sorted.csv │ └── fetal_significant_sorted.csv │ ├── Figure 3 SubClonal Identification.ipynb │ └── GBM Projecting Cancer on Controls.ipynb ├── figure4 ├── Differential_Enhancers_Motifs_Enrichment_Analysis │ ├── diff_enhancers_enriched_motifs.ipynb │ └── helper_utils.py └── PCA_Differential_Enhancers │ ├── README.md │ └── pca_diffenhancers_brca_nncontrol.ipynb ├── figure5 ├── README.md ├── allelic_imbalance │ └── get_vafs.py └── pcawg_variant_prioritization │ ├── README │ ├── mutation_scoring_pipeline │ ├── launch_mutation_centered_scoring.py │ ├── mutation_scoring.py │ └── mutation_scoring.sh │ └── mutation_scoring_pipeline_summit │ ├── launch_summit_centered_scoring.py │ ├── mutation_scoring.py │ └── mutation_scoring.sh └── seq2atac ├── README.md ├── requirements.txt ├── seq2atac ├── __init__.py └── stable │ ├── __init__.py │ ├── analysis.py │ ├── dataloader.py │ ├── models │ ├── __init__.py │ └── convolutional.py │ ├── negative_sampling.py │ ├── shap_utils.py │ ├── train.py │ └── utils.py └── setup.py /README.md: 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