├── .github ├── ISSUE_TEMPLATE │ ├── custom-data-error-template.md │ └── tutorial-error-template.md ├── actions │ ├── conda-build-publish │ │ └── action.yml │ ├── dockerhub-build-publish │ │ └── action.yml │ ├── inference-test-dataset │ │ └── action.yml │ ├── install-bash │ │ └── action.yml │ ├── install-conda │ │ └── action.yml │ └── zenodo-url-translate │ │ └── action.yml ├── dependabot.yml ├── scripts │ └── inference-test-dataset.py └── workflows │ ├── ci-codecheck.yml │ ├── ci-conda.yml │ ├── ci-container.yml │ ├── ci-inference.yml │ ├── ci-install.yml │ └── stale.yml ├── .gitignore ├── INSTALL.md ├── LICENSE ├── README.rst ├── bin ├── dictys └── dictys_helper ├── doc ├── images │ ├── Dictys_overview.png │ ├── Diff_analysis.png │ ├── Dynamic_discovery.png │ ├── Global_dotplot.png │ ├── Global_heatmap.png │ ├── Subnet.png │ ├── animation.gif │ └── logo.png ├── scripts │ └── install.sh └── tutorials │ ├── analysis-blood │ ├── README.md │ └── notebooks │ │ ├── dynamic │ │ ├── discovery.ipynb │ │ └── main.ipynb │ │ └── static │ │ ├── global-dotplot.ipynb │ │ ├── global-heatmap.ipynb │ │ ├── main.ipynb │ │ ├── pair-diff.ipynb │ │ └── subnet.ipynb │ ├── analysis-skin │ ├── README.md │ └── notebooks │ │ └── main.ipynb │ ├── full-multiome │ ├── README.md │ └── notebooks │ │ ├── 0-install.ipynb │ │ ├── 1-data.ipynb │ │ ├── 2-makefile.ipynb │ │ ├── 3-static-inference.ipynb │ │ └── 4-static-analysis.ipynb │ ├── full-skin │ ├── README.md │ └── notebooks │ │ ├── main1.ipynb │ │ └── main2.ipynb │ └── short-multiome │ ├── README.md │ └── notebooks │ └── main.ipynb ├── setup.cfg ├── setup.py ├── src ├── dictys │ ├── __init__.py │ ├── __main__.py │ ├── chromatin.py │ ├── dynamic.py │ ├── net │ │ ├── __init__.py │ │ ├── layout.py │ │ └── stat.py │ ├── network.py │ ├── plot │ │ ├── __init__.py │ │ ├── dynamic.py │ │ ├── layout.py │ │ ├── panel.py │ │ └── static.py │ ├── preproc.py │ ├── scripts │ │ ├── chromatin_homer.py │ │ ├── chromatin_homer.sh │ │ ├── chromatin_macs2.sh │ │ ├── chromatin_wellington.sh │ │ ├── helper │ │ │ ├── expression.py │ │ │ ├── expression_mtx.py │ │ │ ├── gene_gtf.sh │ │ │ ├── genome_homer.sh │ │ │ ├── makefile_check.py │ │ │ ├── makefile_template.sh │ │ │ ├── makefile_update.py │ │ │ ├── motif_homer.sh │ │ │ ├── network_inference.sh │ │ │ ├── repo_dataverse.py │ │ │ ├── repo_zenodo.py │ │ │ ├── repodown.sh │ │ │ ├── split_bam.sh │ │ │ └── split_bam_text.py │ │ └── makefiles │ │ │ ├── common.mk │ │ │ ├── config.mk │ │ │ ├── dynamic.mk │ │ │ ├── env_none.mk │ │ │ ├── env_singularity.mk │ │ │ ├── static.mk │ │ │ ├── test_dynamic.mk │ │ │ └── test_static.mk │ ├── traj.py │ └── utils │ │ ├── __init__.py │ │ ├── file.py │ │ ├── importing.py │ │ ├── networkx.py │ │ ├── numpy.py │ │ ├── parallel.py │ │ └── shell.py └── docstring2argparse │ └── __init__.py └── utils ├── conda └── meta.yaml └── docker ├── Dockerfile └── local └── .placeholder /.github/ISSUE_TEMPLATE/custom-data-error-template.md: 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