CHANGELOG.md
LICENSE
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.py
cooltools/__init__.py
cooltools/__main__.py
cooltools.egg-info/PKG-INFO
cooltools.egg-info/SOURCES.txt
cooltools.egg-info/dependency_links.txt
cooltools.egg-info/entry_points.txt
cooltools.egg-info/not-zip-safe
cooltools.egg-info/requires.txt
cooltools.egg-info/top_level.txt
cooltools/api/__init__.py
cooltools/api/coverage.py
cooltools/api/directionality.py
cooltools/api/dotfinder.py
cooltools/api/eigdecomp.py
cooltools/api/expected.py
cooltools/api/insulation.py
cooltools/api/saddle.py
cooltools/api/sample.py
cooltools/api/snipping.py
cooltools/api/virtual4c.py
cooltools/cli/__init__.py
cooltools/cli/coverage.py
cooltools/cli/dots.py
cooltools/cli/eigs_cis.py
cooltools/cli/eigs_trans.py
cooltools/cli/expected_cis.py
cooltools/cli/expected_trans.py
cooltools/cli/genome.py
cooltools/cli/insulation.py
cooltools/cli/logbin_expected.py
cooltools/cli/pileup.py
cooltools/cli/saddle.py
cooltools/cli/sample.py
cooltools/cli/util.py
cooltools/cli/virtual4c.py
cooltools/lib/__init__.py
cooltools/lib/_numutils.c
cooltools/lib/_numutils.pyx
cooltools/lib/_query.py
cooltools/lib/checks.py
cooltools/lib/common.py
cooltools/lib/io.py
cooltools/lib/numutils.py
cooltools/lib/peaks.py
cooltools/lib/plotting.py
cooltools/lib/runlength.py
cooltools/lib/schemas.py
cooltools/sandbox/__init__.py
cooltools/sandbox/balance.py
cooltools/sandbox/contrast.py
cooltools/sandbox/cool2cworld.py
cooltools/sandbox/cross_score.py
cooltools/sandbox/expected_smoothing.py
cooltools/sandbox/obs_over_exp_cooler.py
cooltools/sandbox/pairs_scaling_functions.py
docs/Makefile
docs/cli.rst
docs/conf.py
docs/cooltools.lib.rst
docs/cooltools.rst
docs/index.rst
docs/make.bat
docs/releases.md
docs/requirements.txt
docs/notebooks_old/01_scaling-curves.ipynb
docs/notebooks_old/02_expected.ipynb
docs/notebooks_old/03_eigendecomposition.ipynb
docs/notebooks_old/04_saddle-plots.ipynb
docs/notebooks_old/05_insulation-score.ipynb
docs/notebooks_old/06_snipping-pileups.ipynb
docs/notebooks_old/07_pileups2.ipynb
docs/notebooks_old/08_dot-calling-internals.ipynb
docs/notebooks_old/data/encode_motifs.hg38.ctcf_known1.liftover.bed.gz
tests/test_call-dots.py
tests/test_checks.py
tests/test_compartments_saddle.py
tests/test_coverage.py
tests/test_dotfinder_chunking.py
tests/test_dotfinder_stats.py
tests/test_expected.py
tests/test_insulation.py
tests/test_io.py
tests/test_lazy_toeplitz.py
tests/test_lib_common.py
tests/test_sample.py
tests/test_snipping.py
tests/test_virtual4c.py
tests/data/CN.mm9.10000kb.cool
tests/data/CN.mm9.1000kb.cool
tests/data/CN.mm9.toy_expected.chromnamed.tsv
tests/data/CN.mm9.toy_expected.tsv
tests/data/CN.mm9.toy_features.bed
tests/data/CN.mm9.toy_regions.bed
tests/data/dotfinder_mock_inputs.npz
tests/data/dotfinder_mock_res.csv.gz
tests/data/make_test_compartments.py
tests/data/mm9.chrom.sizes.reduced
tests/data/mm9.named_nonoverlap_regions.bed
tests/data/sin_eigs_mat.bg2.gz
tests/data/sin_eigs_mat.cool
tests/data/sin_eigs_track.tsv
tests/data/test.10.bins
tests/data/test.chrom.sizes