├── .bumpversion.cfg ├── .gitignore ├── LICENSE ├── README.md ├── conda-devel-env.yml ├── examples └── UsageExamples.ipynb ├── genome_tools ├── __init__.py ├── __main__.py ├── bed.py ├── cli │ └── __init__.py ├── data │ ├── __init__.py │ ├── anndata.py │ ├── dataset.py │ ├── extractors.py │ ├── gc_matching.py │ ├── get_variant_resolved_reads.py │ ├── loaders.py │ ├── pwm.py │ ├── samplers.py │ └── utils.py ├── genomic_interval.py ├── helpers.py ├── hpc │ └── slurm.py ├── plotting │ ├── __init__.py │ ├── colors │ │ ├── __init__.py │ │ ├── cm.py │ │ └── palettes.py │ ├── connectors.py │ ├── contour_plots.py │ ├── gene_annotation.py │ ├── ideogram.py │ ├── modular_plot │ │ ├── README.md │ │ ├── README_develop.md │ │ ├── __init__.py │ │ ├── api.py │ │ ├── example_images │ │ │ ├── GencodeComponent.png │ │ │ ├── IdeogramComponent.png │ │ │ ├── PlotExample1.png │ │ │ ├── PlotExample2.png │ │ │ ├── PlotExample3.png │ │ │ └── TrackComponent.png │ │ ├── interval_plotter.py │ │ ├── loaders │ │ │ ├── __init__.py │ │ │ ├── basic.py │ │ │ ├── dhs.py │ │ │ ├── footprint.py │ │ │ ├── prediction.py │ │ │ ├── sequence.py │ │ │ └── variant.py │ │ ├── plot_components │ │ │ ├── __init__.py │ │ │ ├── abstract.py │ │ │ ├── basic.py │ │ │ ├── dhs.py │ │ │ ├── footprint.py │ │ │ ├── prediction.py │ │ │ ├── sequence.py │ │ │ └── variant.py │ │ └── utils.py │ ├── sequence.py │ └── utils.py └── utils │ ├── __init__.py │ ├── sampling.py │ ├── sequence.py │ └── signal.py ├── pyproject.toml ├── requirements.txt ├── setup.py └── test /.bumpversion.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/.bumpversion.cfg -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/README.md -------------------------------------------------------------------------------- /conda-devel-env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/conda-devel-env.yml -------------------------------------------------------------------------------- /examples/UsageExamples.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/examples/UsageExamples.ipynb -------------------------------------------------------------------------------- /genome_tools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/__init__.py -------------------------------------------------------------------------------- /genome_tools/__main__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /genome_tools/bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/bed.py -------------------------------------------------------------------------------- /genome_tools/cli/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /genome_tools/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/__init__.py -------------------------------------------------------------------------------- /genome_tools/data/anndata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/anndata.py -------------------------------------------------------------------------------- /genome_tools/data/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/dataset.py -------------------------------------------------------------------------------- /genome_tools/data/extractors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/extractors.py -------------------------------------------------------------------------------- /genome_tools/data/gc_matching.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/gc_matching.py -------------------------------------------------------------------------------- /genome_tools/data/get_variant_resolved_reads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/get_variant_resolved_reads.py -------------------------------------------------------------------------------- /genome_tools/data/loaders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/loaders.py -------------------------------------------------------------------------------- /genome_tools/data/pwm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/pwm.py -------------------------------------------------------------------------------- /genome_tools/data/samplers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/samplers.py -------------------------------------------------------------------------------- /genome_tools/data/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/data/utils.py -------------------------------------------------------------------------------- /genome_tools/genomic_interval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/genomic_interval.py -------------------------------------------------------------------------------- /genome_tools/helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/helpers.py -------------------------------------------------------------------------------- /genome_tools/hpc/slurm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/hpc/slurm.py -------------------------------------------------------------------------------- /genome_tools/plotting/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/__init__.py -------------------------------------------------------------------------------- /genome_tools/plotting/colors/__init__.py: -------------------------------------------------------------------------------- 1 | __all__ = ["cm", "palettes"] 2 | -------------------------------------------------------------------------------- /genome_tools/plotting/colors/cm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/colors/cm.py -------------------------------------------------------------------------------- /genome_tools/plotting/colors/palettes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/colors/palettes.py -------------------------------------------------------------------------------- /genome_tools/plotting/connectors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/connectors.py -------------------------------------------------------------------------------- /genome_tools/plotting/contour_plots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/contour_plots.py -------------------------------------------------------------------------------- /genome_tools/plotting/gene_annotation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/gene_annotation.py -------------------------------------------------------------------------------- /genome_tools/plotting/ideogram.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/ideogram.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/README.md -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/README_develop.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/README_develop.md -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/__init__.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/api.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/example_images/GencodeComponent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/example_images/GencodeComponent.png -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/example_images/IdeogramComponent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/example_images/IdeogramComponent.png -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/example_images/PlotExample1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/example_images/PlotExample1.png -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/example_images/PlotExample2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/example_images/PlotExample2.png -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/example_images/PlotExample3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/example_images/PlotExample3.png -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/example_images/TrackComponent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/example_images/TrackComponent.png -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/interval_plotter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/interval_plotter.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/__init__.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/basic.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/dhs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/dhs.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/footprint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/footprint.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/prediction.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/sequence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/sequence.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/loaders/variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/loaders/variant.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/abstract.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/abstract.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/basic.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/dhs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/dhs.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/footprint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/footprint.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/prediction.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/sequence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/sequence.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/plot_components/variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/plot_components/variant.py -------------------------------------------------------------------------------- /genome_tools/plotting/modular_plot/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/modular_plot/utils.py -------------------------------------------------------------------------------- /genome_tools/plotting/sequence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/sequence.py -------------------------------------------------------------------------------- /genome_tools/plotting/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/plotting/utils.py -------------------------------------------------------------------------------- /genome_tools/utils/__init__.py: -------------------------------------------------------------------------------- 1 | __all__ = ["sequence", "sampling"] 2 | -------------------------------------------------------------------------------- /genome_tools/utils/sampling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/utils/sampling.py -------------------------------------------------------------------------------- /genome_tools/utils/sequence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/utils/sequence.py -------------------------------------------------------------------------------- /genome_tools/utils/signal.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/genome_tools/utils/signal.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/vierstralab/genome-tools/HEAD/setup.py -------------------------------------------------------------------------------- /test: -------------------------------------------------------------------------------- 1 | --------------------------------------------------------------------------------