├── .gitignore ├── .snakemake-workflow-catalog.yml ├── LICENSE ├── README.md ├── config ├── test_annotations.tsv ├── test_config.yml ├── test_samples.tsv └── test_samples_annotations.tsv ├── resources ├── README.md ├── genome │ └── hg38_chromsizes.txt └── test_view.txt └── workflow ├── Snakefile ├── envs ├── chromosight_env.yml ├── coolpuppy_env.yml ├── environment.yml ├── hmm_bigwigs_env.yml └── mustache_env.yml ├── report ├── pileups_by_sample.rst ├── pileups_individual.rst └── workflow.rst ├── rules ├── common.smk ├── dots.smk ├── eigenvectors.smk ├── expected.smk ├── insulation_tads.smk ├── pentads.smk ├── pileups.smk └── saddle.smk ├── schemas ├── config.schema.yaml └── samples.schema.yaml └── scripts ├── common.py ├── differential_pentads.py └── merge_pileups.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/quaich/HEAD/.gitignore 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