CHANGELOG.md
LICENSE
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.py
cooltools/__init__.py
cooltools/__main__.py
cooltools/balance.py
cooltools/contrast.py
cooltools/coverage.py
cooltools/directionality.py
cooltools/dotfinder.py
cooltools/eigdecomp.py
cooltools/expected.py
cooltools/insulation.py
cooltools/saddle.py
cooltools/sample.py
cooltools/snipping.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/cli/__init__.py
cooltools/cli/call_compartments.py
cooltools/cli/call_dots.py
cooltools/cli/compute_expected.py
cooltools/cli/compute_saddle.py
cooltools/cli/diamond_insulation.py
cooltools/cli/dump_cworld.py
cooltools/cli/genome.py
cooltools/cli/logbin_expected.py
cooltools/cli/random_sample.py
cooltools/cli/util.py
cooltools/io/__init__.py
cooltools/io/cool2cworld.py
cooltools/io/fastsavetxt.c
cooltools/io/fastsavetxt.pyx
cooltools/lib/__init__.py
cooltools/lib/_numutils.c
cooltools/lib/_numutils.pyx
cooltools/lib/_query.py
cooltools/lib/common.py
cooltools/lib/numutils.py
cooltools/lib/peaks.py
cooltools/lib/plotting.py
cooltools/lib/runlength.py
docs/Makefile
docs/cli.rst
docs/conf.py
docs/cooltools.io.rst
docs/cooltools.lib.rst
docs/cooltools.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/releases.md
docs/requirements.txt
docs/notebooks/01_scaling-curves.ipynb
docs/notebooks/02_expected.ipynb
docs/notebooks/03_eigendecomposition.ipynb
docs/notebooks/04_saddle-plots.ipynb
docs/notebooks/05_insulation-score.ipynb
docs/notebooks/06_snipping-pileups.ipynb
docs/notebooks/07_pileups2.ipynb
docs/notebooks/08_dot-calling-internals.ipynb
docs/notebooks/data/encode_motifs.hg38.ctcf_known1.liftover.bed.gz
tests/test_compartments_saddle.py
tests/test_dotfinder_chunking.py
tests/test_dotfinder_la_exp.py
tests/test_expected.py
tests/test_lazy_toeplitz.py
tests/test_snipping.py
tests/data/CN.mm9.1000kb.cool
tests/data/CN.mm9.toy_expected.tsv
tests/data/CN.mm9.toy_regions.bed
tests/data/make_test_compartments.py
tests/data/mm9.chrom.sizes.reduced
tests/data/mm9.named_nonoverlap_regions.bed
tests/data/mm9.named_overlap_regions.bed
tests/data/mock_inputs.npz
tests/data/mock_res.csv.gz
tests/data/sin_eigs_mat.bg2.gz
tests/data/sin_eigs_mat.cool
tests/data/test.10.bins
tests/data/test.chrom.sizes