.coveragerc
.flake8
.gitignore
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CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
Makefile
README.rst
pyproject.toml
pytest.ini
.github/dependabot.yml
.github/workflows/deploy_coverage.yml
.github/workflows/deploy_documentation.yml
.github/workflows/deploy_release.yml
.github/workflows/quality.yml
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DeepPeak/__init__.py
DeepPeak/_version.py
DeepPeak/benchmarking.py
DeepPeak/directories.py
DeepPeak/pipeline.py
DeepPeak/processing.py
DeepPeak.egg-info/PKG-INFO
DeepPeak.egg-info/SOURCES.txt
DeepPeak.egg-info/dependency_links.txt
DeepPeak.egg-info/requires.txt
DeepPeak.egg-info/top_level.txt
DeepPeak/analysis/__init__.py
DeepPeak/analysis/comparison.py
DeepPeak/analysis/dead_time.py
DeepPeak/analysis/dilution_series.py
DeepPeak/analysis/noise_analysis.py
DeepPeak/analysis/pulse_shape.py
DeepPeak/analysis/series_calculations.py
DeepPeak/analysis/wavenet_trace.py
DeepPeak/analysis/distributions/__init__.py
DeepPeak/analysis/distributions/amplitude.py
DeepPeak/analysis/distributions/event_arrival.py
DeepPeak/analysis/distributions/width.py
DeepPeak/analysis/metrics/__init__.py
DeepPeak/analysis/metrics/config.py
DeepPeak/analysis/metrics/distributions.py
DeepPeak/analysis/metrics/series_result.py
DeepPeak/analysis/metrics/trace_record.py
DeepPeak/analysis/metrics/utils.py
DeepPeak/core/__init__.py
DeepPeak/core/config.py
DeepPeak/core/exceptions.py
DeepPeak/core/protocols.py
DeepPeak/core/types.py
DeepPeak/detection/__init__.py
DeepPeak/detection/base.py
DeepPeak/detection/cholesky_solver.py
DeepPeak/detection/closed_form_solver.py
DeepPeak/detection/non_maximum_suppression.py
DeepPeak/detection/peak_locator.py
DeepPeak/detection/triggers.py
DeepPeak/detection/zero_crossing.py
DeepPeak/generation/__init__.py
DeepPeak/generation/dataset.py
DeepPeak/generation/peak_count.py
DeepPeak/generation/signal_generator.py
DeepPeak/generation/kernels/__init__.py
DeepPeak/generation/kernels/base.py
DeepPeak/generation/kernels/custom.py
DeepPeak/generation/kernels/dirac.py
DeepPeak/generation/kernels/gaussian.py
DeepPeak/generation/kernels/lorentzian.py
DeepPeak/generation/kernels/square.py
DeepPeak/generation/kernels/two_lobe_gaussian.py
DeepPeak/generation/noises/__init__.py
DeepPeak/generation/noises/base.py
DeepPeak/generation/noises/correlated_gaussian.py
DeepPeak/generation/noises/gaussian.py
DeepPeak/generation/noises/laplace.py
DeepPeak/generation/noises/nonstationary_gaussian.py
DeepPeak/io/__init__.py
DeepPeak/io/trace_io.py
DeepPeak/metrics/__init__.py
DeepPeak/models/__init__.py
DeepPeak/models/base.py
DeepPeak/models/dense.py
DeepPeak/models/evaluation.py
DeepPeak/models/losses.py
DeepPeak/models/metrics.py
DeepPeak/models/plotting.py
DeepPeak/models/training.py
DeepPeak/models/unet1d.py
DeepPeak/models/wavenet.py
DeepPeak/plotting/__init__.py
DeepPeak/plotting/trace_plots.py
DeepPeak/plotting/trace_record.py
DeepPeak/utils/__init__.py
DeepPeak/utils/datasets.py
DeepPeak/utils/helper.py
DeepPeak/utils/history.py
DeepPeak/utils/io.py
DeepPeak/utils/iterables.py
DeepPeak/utils/signal_processing.py
DeepPeak/weights/README.rst
DeepPeak/weights/densenet/.gitkeep
DeepPeak/weights/other/.gitkeep
DeepPeak/weights/unet1d/.gitkeep
DeepPeak/weights/unet1d/default-smooth-bce/config.json
DeepPeak/weights/unet1d/default-smooth-bce/history.json
DeepPeak/weights/wavenet/.gitkeep
DeepPeak/weights/wavenet/base-smooth-bce/config.json
DeepPeak/weights/wavenet/base-smooth-bce/history.json
DeepPeak/weights/wavenet/default-smooth-bce/config.json
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DeepPeak/weights/wavenet/regression-shape-aware/config.json
DeepPeak/weights/wavenet/regression-shape-aware/history.json
conda.recipe/meta.yaml
docs/make.bat
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docs/examples/classifier_wavenet.py
docs/examples/core_result_objects.py
docs/examples/data_generation.py
docs/examples/data_generation_custom_kernel.py
docs/examples/neural_losses.py
docs/examples/noise_and_pulse_analysis.py
docs/examples/non_maximum_suppression.py
docs/examples/pretrained_weights.py
docs/examples/pulse_kernel_extraction.py
docs/examples/wavenet_realistic_training.py
docs/images/logo.svg
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docs/source/conf.py
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docs/source/index.rst
docs/source/migration.rst
docs/source/model_card.rst
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docs/source/guides/synthetic_traces.rst
docs/source/guides/train_wavenet.rst
notebooks/deeppeak_tutorial.ipynb
notebooks/.ipynb_checkpoints/processing_signal-checkpoint.ipynb
notebooks/.ipynb_checkpoints/wavenet_training-checkpoint.ipynb
showcase/webinar/README.md
showcase/webinar/amsterdam-umc-logo-presentation.png
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showcase/webinar/build_presentation.applescript
showcase/webinar/build_presentation.py
showcase/webinar/cyto-amplitudes.png
showcase/webinar/cyto-arrival-time.png
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tests/__init__.py
tests/conftest.py
tests/test_amplitude_analysis.py
tests/test_analysis_errors.py
tests/test_architecture.py
tests/test_benchmarking.py
tests/test_classifiers.py
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tests/test_noise_generation.py
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tools/check_release.py
tools/next_release_version.py
tools/release_tag.py
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