├── .coveragerc ├── .flake8 ├── .github └── workflows │ ├── pypi-publish.yml │ ├── pytest.yml │ └── python-publish-test.yml ├── .gitignore ├── .readthedocs.yml ├── .zenodo.json ├── CHANGELOG.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── cooltools ├── __init__.py ├── __main__.py ├── api │ ├── __init__.py │ ├── coverage.py │ ├── directionality.py │ ├── dotfinder.py │ ├── eigdecomp.py │ ├── expected.py │ ├── insulation.py │ ├── rearrange.py │ ├── saddle.py │ ├── sample.py │ ├── snipping.py │ └── virtual4c.py ├── cli │ ├── __init__.py │ ├── coverage.py │ ├── dots.py │ ├── eigs_cis.py │ ├── eigs_trans.py │ ├── expected_cis.py │ ├── expected_trans.py │ ├── genome.py │ ├── insulation.py │ ├── logbin_expected.py │ ├── pileup.py │ ├── rearrange.py │ ├── saddle.py │ ├── sample.py │ ├── util.py │ └── virtual4c.py ├── lib │ ├── __init__.py │ ├── _numutils.pyx │ ├── _query.py │ ├── checks.py │ ├── common.py │ ├── io.py │ ├── numutils.py │ ├── peaks.py │ ├── plotting.py │ ├── runlength.py │ └── schemas.py └── sandbox │ ├── __init__.py │ ├── balance.py │ ├── contrast.py │ ├── cool2cworld.py │ ├── cooler_filters │ ├── Example_usage.ipynb │ ├── pixel_filter_util.py │ └── test_data_util.cool │ ├── cross_score.py │ ├── expected_smoothing.py │ ├── expected_smoothing_example.ipynb │ ├── fastsavetxt.pyx │ ├── obs_over_exp_cooler.py │ ├── observed_over_expected_example.ipynb │ ├── pairs_scaling_functions.py │ └── rearrange_cooler_example.ipynb ├── datasets └── external_test_files.tsv ├── docs ├── Makefile ├── cli.rst ├── conf.py ├── cooltools.lib.rst ├── cooltools.rst ├── figs │ └── cooltools-logo-futura.png ├── index.rst ├── make.bat ├── notebooks_old │ ├── 01_scaling-curves.ipynb │ ├── 02_expected.ipynb │ ├── 03_eigendecomposition.ipynb │ ├── 04_saddle-plots.ipynb │ ├── 05_insulation-score.ipynb │ ├── 06_snipping-pileups.ipynb │ ├── 07_pileups2.ipynb │ ├── 08_dot-calling-internals.ipynb │ └── data │ │ └── encode_motifs.hg38.ctcf_known1.liftover.bed.gz ├── releases.md └── requirements.txt ├── pyproject.toml ├── pytest.ini ├── requirements-dev.txt ├── requirements.txt ├── setup.py └── tests ├── data ├── CN.mm9.10000kb.cool ├── CN.mm9.1000kb.cool ├── CN.mm9.toy_expected.chromnamed.tsv ├── CN.mm9.toy_expected.tsv ├── CN.mm9.toy_features.bed ├── CN.mm9.toy_regions.bed ├── dotfinder_mock_inputs.npz ├── dotfinder_mock_res.csv.gz ├── float_counts.cool ├── make_test_compartments.py ├── mm9.chrom.sizes.reduced ├── mm9.named_nonoverlap_regions.bed ├── sin_eigs_mat.bg2.gz ├── sin_eigs_mat.cool ├── sin_eigs_track.tsv ├── test.10.bins └── test.chrom.sizes ├── test_call-dots.py ├── test_checks.py ├── test_compartments_saddle.py ├── test_coverage.py ├── test_dotfinder_chunking.py ├── test_dotfinder_stats.py ├── test_expected.py ├── test_insulation.py ├── test_io.py ├── test_lazy_toeplitz.py ├── test_lib_common.py ├── test_rearrange_cooler.py ├── test_sample.py ├── test_snipping.py └── test_virtual4c.py /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.coveragerc -------------------------------------------------------------------------------- /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.flake8 -------------------------------------------------------------------------------- /.github/workflows/pypi-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.github/workflows/pypi-publish.yml -------------------------------------------------------------------------------- /.github/workflows/pytest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.github/workflows/pytest.yml -------------------------------------------------------------------------------- /.github/workflows/python-publish-test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.github/workflows/python-publish-test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.readthedocs.yml -------------------------------------------------------------------------------- /.zenodo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/.zenodo.json -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/README.md -------------------------------------------------------------------------------- /cooltools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/__init__.py -------------------------------------------------------------------------------- /cooltools/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/__main__.py -------------------------------------------------------------------------------- /cooltools/api/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/__init__.py -------------------------------------------------------------------------------- /cooltools/api/coverage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/coverage.py -------------------------------------------------------------------------------- /cooltools/api/directionality.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/directionality.py -------------------------------------------------------------------------------- /cooltools/api/dotfinder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/dotfinder.py -------------------------------------------------------------------------------- /cooltools/api/eigdecomp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/eigdecomp.py -------------------------------------------------------------------------------- /cooltools/api/expected.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/expected.py -------------------------------------------------------------------------------- /cooltools/api/insulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/insulation.py -------------------------------------------------------------------------------- /cooltools/api/rearrange.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/rearrange.py -------------------------------------------------------------------------------- /cooltools/api/saddle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/saddle.py -------------------------------------------------------------------------------- /cooltools/api/sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/sample.py -------------------------------------------------------------------------------- /cooltools/api/snipping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/snipping.py -------------------------------------------------------------------------------- /cooltools/api/virtual4c.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/api/virtual4c.py -------------------------------------------------------------------------------- /cooltools/cli/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/__init__.py -------------------------------------------------------------------------------- /cooltools/cli/coverage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/coverage.py -------------------------------------------------------------------------------- /cooltools/cli/dots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/dots.py -------------------------------------------------------------------------------- /cooltools/cli/eigs_cis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/eigs_cis.py -------------------------------------------------------------------------------- /cooltools/cli/eigs_trans.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/eigs_trans.py -------------------------------------------------------------------------------- /cooltools/cli/expected_cis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/expected_cis.py -------------------------------------------------------------------------------- /cooltools/cli/expected_trans.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/expected_trans.py -------------------------------------------------------------------------------- /cooltools/cli/genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/genome.py -------------------------------------------------------------------------------- /cooltools/cli/insulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/insulation.py -------------------------------------------------------------------------------- /cooltools/cli/logbin_expected.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/logbin_expected.py -------------------------------------------------------------------------------- /cooltools/cli/pileup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/pileup.py -------------------------------------------------------------------------------- /cooltools/cli/rearrange.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/rearrange.py -------------------------------------------------------------------------------- /cooltools/cli/saddle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/saddle.py -------------------------------------------------------------------------------- /cooltools/cli/sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/sample.py -------------------------------------------------------------------------------- /cooltools/cli/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/util.py -------------------------------------------------------------------------------- /cooltools/cli/virtual4c.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/cli/virtual4c.py -------------------------------------------------------------------------------- /cooltools/lib/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/__init__.py -------------------------------------------------------------------------------- /cooltools/lib/_numutils.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/_numutils.pyx -------------------------------------------------------------------------------- /cooltools/lib/_query.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/_query.py -------------------------------------------------------------------------------- /cooltools/lib/checks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/checks.py -------------------------------------------------------------------------------- /cooltools/lib/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/common.py -------------------------------------------------------------------------------- /cooltools/lib/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/io.py -------------------------------------------------------------------------------- /cooltools/lib/numutils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/numutils.py -------------------------------------------------------------------------------- /cooltools/lib/peaks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/peaks.py -------------------------------------------------------------------------------- /cooltools/lib/plotting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/plotting.py -------------------------------------------------------------------------------- /cooltools/lib/runlength.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/runlength.py -------------------------------------------------------------------------------- /cooltools/lib/schemas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/lib/schemas.py -------------------------------------------------------------------------------- /cooltools/sandbox/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cooltools/sandbox/balance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/balance.py -------------------------------------------------------------------------------- /cooltools/sandbox/contrast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/contrast.py -------------------------------------------------------------------------------- /cooltools/sandbox/cool2cworld.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/cool2cworld.py -------------------------------------------------------------------------------- /cooltools/sandbox/cooler_filters/Example_usage.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/cooler_filters/Example_usage.ipynb -------------------------------------------------------------------------------- /cooltools/sandbox/cooler_filters/pixel_filter_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/cooler_filters/pixel_filter_util.py -------------------------------------------------------------------------------- /cooltools/sandbox/cooler_filters/test_data_util.cool: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/cooler_filters/test_data_util.cool -------------------------------------------------------------------------------- /cooltools/sandbox/cross_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/cross_score.py -------------------------------------------------------------------------------- /cooltools/sandbox/expected_smoothing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/expected_smoothing.py -------------------------------------------------------------------------------- /cooltools/sandbox/expected_smoothing_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/expected_smoothing_example.ipynb -------------------------------------------------------------------------------- /cooltools/sandbox/fastsavetxt.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/fastsavetxt.pyx -------------------------------------------------------------------------------- /cooltools/sandbox/obs_over_exp_cooler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/obs_over_exp_cooler.py -------------------------------------------------------------------------------- /cooltools/sandbox/observed_over_expected_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/observed_over_expected_example.ipynb -------------------------------------------------------------------------------- /cooltools/sandbox/pairs_scaling_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/pairs_scaling_functions.py -------------------------------------------------------------------------------- /cooltools/sandbox/rearrange_cooler_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/cooltools/sandbox/rearrange_cooler_example.ipynb -------------------------------------------------------------------------------- /datasets/external_test_files.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/datasets/external_test_files.tsv -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/cli.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/cooltools.lib.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/cooltools.lib.rst -------------------------------------------------------------------------------- /docs/cooltools.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/cooltools.rst -------------------------------------------------------------------------------- /docs/figs/cooltools-logo-futura.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/figs/cooltools-logo-futura.png -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/notebooks_old/01_scaling-curves.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/01_scaling-curves.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/02_expected.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/02_expected.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/03_eigendecomposition.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/03_eigendecomposition.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/04_saddle-plots.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/04_saddle-plots.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/05_insulation-score.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/05_insulation-score.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/06_snipping-pileups.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/06_snipping-pileups.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/07_pileups2.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/07_pileups2.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/08_dot-calling-internals.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/08_dot-calling-internals.ipynb -------------------------------------------------------------------------------- /docs/notebooks_old/data/encode_motifs.hg38.ctcf_known1.liftover.bed.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/notebooks_old/data/encode_motifs.hg38.ctcf_known1.liftover.bed.gz -------------------------------------------------------------------------------- /docs/releases.md: -------------------------------------------------------------------------------- 1 | ../CHANGELOG.md -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/pyproject.toml -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/pytest.ini -------------------------------------------------------------------------------- /requirements-dev.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/requirements-dev.txt -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/setup.py -------------------------------------------------------------------------------- /tests/data/CN.mm9.10000kb.cool: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/CN.mm9.10000kb.cool -------------------------------------------------------------------------------- /tests/data/CN.mm9.1000kb.cool: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/CN.mm9.1000kb.cool -------------------------------------------------------------------------------- /tests/data/CN.mm9.toy_expected.chromnamed.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/CN.mm9.toy_expected.chromnamed.tsv -------------------------------------------------------------------------------- /tests/data/CN.mm9.toy_expected.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/CN.mm9.toy_expected.tsv -------------------------------------------------------------------------------- /tests/data/CN.mm9.toy_features.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/CN.mm9.toy_features.bed -------------------------------------------------------------------------------- /tests/data/CN.mm9.toy_regions.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/CN.mm9.toy_regions.bed -------------------------------------------------------------------------------- /tests/data/dotfinder_mock_inputs.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/dotfinder_mock_inputs.npz -------------------------------------------------------------------------------- /tests/data/dotfinder_mock_res.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/dotfinder_mock_res.csv.gz -------------------------------------------------------------------------------- /tests/data/float_counts.cool: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/float_counts.cool -------------------------------------------------------------------------------- /tests/data/make_test_compartments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/make_test_compartments.py -------------------------------------------------------------------------------- /tests/data/mm9.chrom.sizes.reduced: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/mm9.chrom.sizes.reduced -------------------------------------------------------------------------------- /tests/data/mm9.named_nonoverlap_regions.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/mm9.named_nonoverlap_regions.bed -------------------------------------------------------------------------------- /tests/data/sin_eigs_mat.bg2.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/sin_eigs_mat.bg2.gz -------------------------------------------------------------------------------- /tests/data/sin_eigs_mat.cool: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/sin_eigs_mat.cool -------------------------------------------------------------------------------- /tests/data/sin_eigs_track.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/sin_eigs_track.tsv -------------------------------------------------------------------------------- /tests/data/test.10.bins: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/test.10.bins -------------------------------------------------------------------------------- /tests/data/test.chrom.sizes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/data/test.chrom.sizes -------------------------------------------------------------------------------- /tests/test_call-dots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_call-dots.py -------------------------------------------------------------------------------- /tests/test_checks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_checks.py -------------------------------------------------------------------------------- /tests/test_compartments_saddle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_compartments_saddle.py -------------------------------------------------------------------------------- /tests/test_coverage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_coverage.py -------------------------------------------------------------------------------- /tests/test_dotfinder_chunking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_dotfinder_chunking.py -------------------------------------------------------------------------------- /tests/test_dotfinder_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_dotfinder_stats.py -------------------------------------------------------------------------------- /tests/test_expected.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_expected.py -------------------------------------------------------------------------------- /tests/test_insulation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_insulation.py -------------------------------------------------------------------------------- /tests/test_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_io.py -------------------------------------------------------------------------------- /tests/test_lazy_toeplitz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_lazy_toeplitz.py -------------------------------------------------------------------------------- /tests/test_lib_common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_lib_common.py -------------------------------------------------------------------------------- /tests/test_rearrange_cooler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_rearrange_cooler.py -------------------------------------------------------------------------------- /tests/test_sample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_sample.py -------------------------------------------------------------------------------- /tests/test_snipping.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_snipping.py -------------------------------------------------------------------------------- /tests/test_virtual4c.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/open2c/cooltools/HEAD/tests/test_virtual4c.py --------------------------------------------------------------------------------