├── .editorconfig ├── .github └── workflows │ ├── os_mac.yml │ ├── os_ubuntu.yml │ ├── os_windows.yml │ ├── python-package-conda.yml │ ├── python27-package.yml │ ├── python36-package.yml │ ├── python37-package.yml │ ├── python38-package.yml │ └── python39-package.yml ├── .gitignore ├── .readthedocs.yml ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── System_Requirements.rst ├── _static │ └── css │ │ └── custom.css ├── _templates │ └── autosummary │ │ ├── base.rst │ │ └── class.rst ├── api │ └── index.rst ├── basic_usage.rst ├── conf.py ├── examples.rst ├── index.rst ├── installation.rst ├── make.bat ├── pictures │ ├── Buenrostro_umap.png │ ├── heatmap.png │ ├── pbmc_PCA_coverage.png │ ├── pbmc_diffmap.png │ ├── pbmc_umap.png │ ├── umap.png │ ├── umapSatb2_CLUSTER_NORM.png │ ├── umap_ATACseq_Astrocyte_marker.png │ ├── umap_markers_hodology_ecker.png │ ├── umapenhancer_CG_Luoetal.png │ └── umapexcitatory_neurons_promoters.png ├── references.rst ├── release_notes.rst ├── requirements.txt └── tutorials │ ├── ATAC_bld_ct_mtx_tutorial.html │ ├── Buenrostro_PBMC_data_processing.html │ ├── Buenrostro_PBMC_data_processing.ipynb │ ├── Cusanovich2018_BoneMarrow_data_processing_diffmap.html │ ├── Tutorial-preprocessing_ATAC_cusanovich.html │ ├── Tutorial_Hackathon_Buenrostro_2.html │ ├── Tutorial_building_custom_count_matrices_from_tsv_or_cellranger_outputs.html │ ├── Tutorial_building_custom_count_matrices_from_tsv_or_cellranger_outputs.ipynb │ ├── beta_tutorial_10x_pbmc.html │ ├── bld_count_matrix_methylation_tutorial.html │ ├── processing_enhancers_mCG.html │ ├── processing_enhancers_mCG.ipynb │ ├── snap2anndata │ ├── = │ ├── SnapATAC_to_anndata_March26th2020.html │ └── SnapATAC_to_anndata_March26th2020.ipynb │ ├── tutorial_atac_pbmc_5k_nextgem.ipynb │ ├── tutorial_build_10x_ct_mtx.ipynb │ └── tutorial_satpathy_et_al.ipynb ├── environment.yml ├── episcanpy ├── __init__.py ├── _compat.py ├── _multidata.py ├── _settings.py ├── _version.py ├── api │ ├── __init__.py │ ├── ct.py │ ├── functions.py │ ├── pl.py │ ├── pp.py │ └── tl.py ├── count_matrix │ ├── __init__.py │ ├── _atac_mtx.py │ ├── _bld_atac_mtx.py │ ├── _bld_atac_mtx_parallel.py │ ├── _bld_met_mtx.py │ ├── _extract.py │ ├── _features.py │ ├── _load_input_file.py │ ├── _load_met_ct_mtx.py │ ├── _peak_fct.py │ └── _read_meth_file.py ├── functions │ ├── __init__.py │ ├── _extract_meth.py │ └── _load_features.py ├── logging.py ├── plotting │ ├── __init__.py │ ├── _heatmap.py │ ├── _histograms.py │ ├── _scanpy_plotting.py │ ├── _scanpy_quality.py │ ├── _silhouette.py │ ├── _variable_features.py │ └── _violin.py ├── preprocessing │ ├── __init__.py │ ├── _correlation_components.py │ ├── _decomposition.py │ ├── _episcanpy_mo_fcts.py │ ├── _extract.py │ ├── _gtf_file_fct.py │ ├── _kneedle.py │ ├── _load_atac.py │ ├── _load_matrix.py │ ├── _metadata.py │ ├── _neighbors.py │ ├── _nucleosome_signal.py │ ├── _quality_control.py │ ├── _readimpute.py │ ├── _recipe.py │ ├── _scanpy_fct.py │ ├── _simple.py │ ├── _snapatac2anndata.py │ ├── _tss_enrichment.py │ └── notes_benchmarking_multiomic.R ├── settings.py ├── tools │ ├── __init__.py │ ├── _cell_id.py │ ├── _clustering.py │ ├── _comparisons.py │ ├── _enrichment_analysis.py │ ├── _features_selection.py │ ├── _find_genes.py │ ├── _find_genes2.py │ ├── _footprinting.py │ ├── _geneactivity.py │ ├── _impute_gene_methylation.py │ ├── _impute_meth.py │ ├── _lsi.py │ ├── _motif_search.py │ ├── _recipe.py │ ├── _scanpy_fct.py │ ├── _scanpy_fct_features.py │ ├── _silhouette.py │ └── _top_feature_genes.py └── utils.py ├── requirements.txt ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── pytest.ini └── test_loading_episcanpy.py ├── umapenhancer_CG_Luoetal.png └── versioneer.py /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/colomemaria/epiScanpy/HEAD/.editorconfig 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