├── .DS_Store ├── .gitignore ├── README.md ├── chromograph.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── chromograph ├── .DS_Store ├── CNV │ ├── Karyotyper.py │ ├── __pycache__ │ │ └── Karyotyper.cpython-37.pyc │ └── setup.R ├── RNA │ ├── FeatureSelectionByMultilevelEnrichment.py │ ├── RNA_analysis.py │ ├── __pycache__ │ │ ├── FeatureSelectionByMultilevelEnrichment.cpython-37.pyc │ │ ├── RNA_analysis.cpython-37.pyc │ │ └── utils.cpython-37.pyc │ └── utils.py ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-37.pyc │ ├── __init__.cpython-38.pyc │ ├── _version.cpython-36.pyc │ ├── _version.cpython-37.pyc │ └── _version.cpython-38.pyc ├── _version.py ├── cicero │ ├── __pycache__ │ │ ├── cicero.cpython-36.pyc │ │ ├── cicero.cpython-37.pyc │ │ ├── generate_Coaccessibilty_networks.cpython-36.pyc │ │ ├── generate_Coaccessibilty_networks.cpython-37.pyc │ │ └── run_cicero.cpython-36.pyc │ ├── cicero.py │ ├── generate_Coaccessibilty_networks.py │ ├── run_cicero.py │ └── utils.py ├── features │ ├── .ipynb_checkpoints │ │ ├── bin_annotation-checkpoint.py │ │ ├── feature_count-checkpoint.py │ │ └── gene_accessibility-checkpoint.py │ ├── GA_Aggregator.py │ ├── Generate_promoter.py │ ├── __pycache__ │ │ ├── GA_Aggregator.cpython-37.pyc │ │ ├── Generate_promoter.cpython-37.pyc │ │ ├── bin_annotation.cpython-37.pyc │ │ ├── count_genes.cpython-37.pyc │ │ ├── feature_count.cpython-37.pyc │ │ ├── gene_smooth.cpython-37.pyc │ │ └── utils.cpython-37.pyc │ ├── bin_annotation.py │ ├── feature_count.py │ ├── gene_accessibility.py │ ├── gene_smooth.py │ └── utils.py ├── motifs │ ├── __pycache__ │ │ ├── motif_aggregation.cpython-37.pyc │ │ └── motif_compounder.cpython-37.pyc │ ├── motif_aggregation.py │ └── motif_compounder.py ├── peak_analysis │ ├── Peak_Aggregator.py │ ├── __pycache__ │ │ ├── Peak_Aggregator.cpython-37.pyc │ │ ├── feature_selection_by_PearsonResiduals.cpython-37.pyc │ │ ├── feature_selection_by_variance.cpython-37.pyc │ │ ├── peak_analysis.cpython-37.pyc │ │ ├── peak_clustering.cpython-37.pyc │ │ ├── utils.cpython-36.pyc │ │ └── utils.cpython-37.pyc │ ├── feature_selection_by_PearsonResiduals.py │ ├── feature_selection_by_variance.py │ ├── peak_analysis.py │ ├── peak_clustering.py │ └── utils.py ├── peak_calling │ ├── .ipynb_checkpoints │ │ ├── call_MACS-checkpoint.py │ │ ├── peak_caller-checkpoint.py │ │ └── utils-checkpoint.py │ ├── __pycache__ │ │ ├── call_MACS.cpython-37.pyc │ │ ├── peak_caller.cpython-37.pyc │ │ ├── utils.cpython-36.pyc │ │ └── utils.cpython-37.pyc │ ├── call_MACS.py │ ├── generate_homer_motifs.py │ ├── peak_caller.py │ └── utils.py ├── pipeline │ ├── .ipynb_checkpoints │ │ ├── Bin_analysis-checkpoint.py │ │ ├── Workflow-checkpoint.py │ │ ├── config-checkpoint.py │ │ ├── merge_analyse-checkpoint.py │ │ └── messy_workflow-checkpoint.ipynb │ ├── Add_UMAP.py │ ├── Bin_analysis.py │ ├── PCA.py │ ├── Pool_split.py │ ├── Pool_workflow.py │ ├── RNA_workflow.py │ ├── SVD.py │ ├── Split_subset.py │ ├── TF_IDF.py │ ├── __pycache__ │ │ ├── Add_UMAP.cpython-37.pyc │ │ ├── Bin_analysis.cpython-37.pyc │ │ ├── Bin_analysis.cpython-38.pyc │ │ ├── PCA.cpython-37.pyc │ │ ├── Pool_split.cpython-37.pyc │ │ ├── SVD.cpython-37.pyc │ │ ├── Split_subset.cpython-37.pyc │ │ ├── TF_IDF.cpython-36.pyc │ │ ├── TF_IDF.cpython-37.pyc │ │ ├── config.cpython-37.pyc │ │ ├── peak_analysis.cpython-37.pyc │ │ ├── utils.cpython-36.pyc │ │ └── utils.cpython-37.pyc │ ├── config.py │ ├── main_workflow.py │ ├── subset_workflow.py │ └── utils.py ├── plotting │ ├── .ipynb_checkpoints │ │ ├── QC_plot-checkpoint.py │ │ └── marker_plot-checkpoint.py │ ├── QC_plot.py │ ├── __pycache__ │ │ ├── QC_plot.cpython-36.pyc │ │ ├── QC_plot.cpython-37.pyc │ │ ├── UMI_plot.cpython-37.pyc │ │ ├── bigwig_plot.cpython-37.pyc │ │ ├── marker_plot.cpython-37.pyc │ │ ├── motif_heatmap.cpython-37.pyc │ │ ├── motif_plot.cpython-37.pyc │ │ ├── peak_annotation_plot.cpython-37.pyc │ │ ├── sample_QC_plot.cpython-37.pyc │ │ └── sample_distribution_plot.cpython-37.pyc │ ├── bigwig_plot.py │ ├── marker_plot.py │ ├── motif_heatmap.py │ ├── motif_plot.py │ ├── peak_annotation_plot.py │ ├── sample_QC_plot.py │ └── sample_distribution_plot.py ├── preprocessing │ ├── .ipynb_checkpoints │ │ ├── Chromgen-checkpoint.py │ │ ├── Generate_GA_ref-checkpoint.py │ │ ├── Generate_TF_reference-checkpoint.py │ │ ├── bin_generation-checkpoint.py │ │ ├── bin_smooth-checkpoint.py │ │ └── utils-checkpoint.py │ ├── Chromgen.py │ ├── Generate_GA_ref.py │ ├── Generate_TF_reference.py │ ├── __pycache__ │ │ ├── Chromgen.cpython-37.pyc │ │ ├── bin_generation.cpython-36.pyc │ │ ├── bin_generation.cpython-37.pyc │ │ ├── doublet_finder.cpython-37.pyc │ │ ├── utils.cpython-36.pyc │ │ └── utils.cpython-37.pyc │ ├── bin_generation.py │ ├── bin_smooth.py │ ├── chromgen_workflow.py │ ├── doublet_finder.py │ └── utils.py └── references │ ├── .ipynb_checkpoints │ ├── human_TFs-checkpoint.motifs │ └── male.GRCh38.chrom-checkpoint.sizes │ ├── GRCh38_2kbprom.bed │ ├── GRCh38_2kbprom_test.bed │ ├── GRCh38_genes_2kbprom.bed │ ├── blacklist_GRCh38.bed │ ├── blacklist_hg19.bed │ ├── blacklist_mm10.bed │ ├── chromosome_arm_positions_grch38.txt │ ├── human_TFs.motifs │ ├── human_TFs_old.motifs │ ├── male.GRCh38.chrom.sizes │ ├── male.hg19.chrom.sizes │ └── male.mm10.chrom.sizes └── setup.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linnarsson-lab/chromograph/HEAD/.DS_Store -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | notebooks/* 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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