├── .gitattributes ├── .github └── workflows │ ├── install_lint_test.yml │ └── publish.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── docs ├── Fig_workflow.png ├── Fig_workflow2.png ├── commands.md ├── index.md ├── make_commands_md.sh ├── scbs_tutorial_data │ ├── Mus_musculus.GRCm38.102_TSS.bed │ ├── cell_01.cov │ ├── cell_02.cov │ ├── cell_03.cov │ ├── cell_04.cov │ ├── cell_05.cov │ ├── cell_06.cov │ ├── cell_07.cov │ ├── cell_08.cov │ ├── cell_09.cov │ ├── cell_10.cov │ ├── cell_11.cov │ ├── cell_12.cov │ ├── cell_13.cov │ ├── cell_14.cov │ ├── cell_15.cov │ ├── cell_16.cov │ ├── cell_17.cov │ ├── cell_18.cov │ ├── cell_19.cov │ ├── cell_20.cov │ ├── cell_21.cov │ ├── cell_22.cov │ ├── cell_23.cov │ ├── cell_24.cov │ ├── cell_25.cov │ ├── cell_26.cov │ ├── cell_27.cov │ ├── cell_28.cov │ ├── cell_29.cov │ ├── cell_30.cov │ └── mouse_promoters.bed ├── tutorial.md ├── tutorial_PCA.png ├── tutorial_PCA_promoter.png ├── tutorial_QC.png ├── tutorial_UMAP.png ├── tutorial_UMAP_clusters.png ├── tutorial_scan_params.png └── tutorial_tss_profiles.png ├── methscan ├── __init__.py ├── cli.py ├── diff.py ├── filter.py ├── matrix.py ├── numerics.py ├── prepare.py ├── profile.py ├── scan.py ├── smooth.py └── utils.py ├── poetry.lock ├── pyproject.toml └── tests ├── __init__.py ├── data ├── Mus_musculus.GRCm38.102_TSS.bed ├── bismark_5_cells │ ├── AS-485320-LR-51079_subset.NOMe.CpG.cov │ ├── AS-485322-LR-51079_subset.NOMe.CpG.cov │ ├── AS-485324-LR-51079_subset.NOMe.CpG.cov.gz │ ├── AS-485326-LR-51079_subset.NOMe.CpG.cov │ └── AS-485338-LR-51079_subset.NOMe.CpG.cov ├── coo_chunks │ ├── 1_chunk0000000.coo │ ├── 1_chunk0000001.coo │ └── 1_chunk0000002.coo ├── tiny │ ├── a.cov │ ├── b.cov.gz │ ├── data_dir │ │ ├── 1.npz │ │ ├── 2.npz │ │ ├── cell_stats.csv │ │ ├── column_header.txt │ │ └── run_info.txt │ └── data_dir_smooth │ │ ├── 1.npz │ │ ├── 2.npz │ │ ├── cell_stats.csv │ │ ├── column_header.txt │ │ └── smoothed │ │ ├── 1.csv │ │ └── 2.csv ├── tiny_custom │ ├── a.cov │ └── b.cov.gz └── tiny_diff │ ├── .DS_Store │ ├── 1.npz │ ├── 10.npz │ ├── 11.npz │ ├── 12.npz │ ├── 13.npz │ ├── 14.npz │ ├── 15.npz │ ├── 16.npz │ ├── 17.npz │ ├── 18.npz │ ├── 19.npz │ ├── 2.npz │ ├── 3.npz │ ├── 4.npz │ ├── 5.npz │ ├── 6.npz │ ├── 7.npz │ ├── 8.npz │ ├── 9.npz │ ├── X.npz │ ├── Y.npz │ ├── cell_groups.csv │ ├── cell_groups_alt.csv │ ├── cell_stats.csv │ ├── column_header.txt │ ├── run_info.txt │ └── smoothed │ ├── 1.csv │ ├── 10.csv │ ├── 11.csv │ ├── 12.csv │ ├── 13.csv │ ├── 14.csv │ ├── 15.csv │ ├── 16.csv │ ├── 17.csv │ ├── 18.csv │ ├── 19.csv │ ├── 2.csv │ ├── 3.csv │ ├── 4.csv │ ├── 5.csv │ ├── 6.csv │ ├── 7.csv │ ├── 8.csv │ ├── 9.csv │ ├── X.csv │ └── Y.csv ├── test_cli.py ├── test_diff.py ├── test_prepare.py ├── test_scan.py └── test_version.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/anders-biostat/MethSCAn/HEAD/.gitattributes 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