LICENSE
README.rst
pyproject.toml
setup.cfg
encode_analysis/__init__.py
mutopia/__init__.py
mutopia/feature_preprocessing.py
mutopia/palettes.py
mutopia/simulate.py
mutopia/tuning.py
mutopia/utils.py
mutopia.egg-info/PKG-INFO
mutopia.egg-info/SOURCES.txt
mutopia.egg-info/dependency_links.txt
mutopia.egg-info/entry_points.txt
mutopia.egg-info/requires.txt
mutopia.egg-info/top_level.txt
mutopia.egg-info/zip-safe
mutopia/analysis/__init__.py
mutopia/cli/__init__.py
mutopia/cli/gensor_core.py
mutopia/cli/gtensor_cli.py
mutopia/cli/model_cli.py
mutopia/cli/model_core.py
mutopia/cli/pipeline_config.py
mutopia/cli/pipeline_tasks.py
mutopia/cli/sbs_cli.py
mutopia/genome_utils/__init__.py
mutopia/genome_utils/bed12_utils.py
mutopia/genome_utils/fancy_iterators.py
mutopia/gtensor/__init__.py
mutopia/gtensor/disk_interface.py
mutopia/gtensor/dtypes.py
mutopia/gtensor/gtensor.py
mutopia/gtensor/interfaces.py
mutopia/gtensor/validation.py
mutopia/gtensor/xarr_extensions.py
mutopia/ingestion/__init__.py
mutopia/ingestion/base.py
mutopia/ingestion/features.py
mutopia/ingestion/gene_features.py
mutopia/ingestion/gtf_parsing.py
mutopia/ingestion/regions.py
mutopia/modalities/__init__.py
mutopia/modalities/mode_config.py
mutopia/modalities/sbs/__init__.py
mutopia/modalities/sbs/_sbs_clustering.py
mutopia/modalities/sbs/_sbs_ingestion.py
mutopia/modalities/sbs/_sbs_nucdata.py
mutopia/modalities/sbs/context_only_model.py
mutopia/modalities/sbs/model.py
mutopia/modalities/sbs/musical_sbs.json
mutopia/modalities/sbs/sbs.py
mutopia/model/__init__.py
mutopia/model/base.py
mutopia/model/mixture_model/__init__.py
mutopia/model/mixture_model/base.py
mutopia/model/mixture_model/dense_mixture_locals.py
mutopia/model/mixture_model/mixture_interface.py
mutopia/model/mixture_model/sampling.py
mutopia/model/mixture_model/sparse_mixture_locals.py
mutopia/model/model/__init__.py
mutopia/model/model/factor_model.py
mutopia/model/model/gtensor_interface.py
mutopia/model/model/optim.py
mutopia/model/model/latent_var_models/__init__.py
mutopia/model/model/latent_var_models/_dirichlet_update.py
mutopia/model/model/latent_var_models/base.py
mutopia/model/model/latent_var_models/dense_lda_locals.py
mutopia/model/model/latent_var_models/sparse_lda_locals.py
mutopia/model/model/model_components/__init__.py
mutopia/model/model/model_components/_fast_eln.py
mutopia/model/model/model_components/_feature_tranformer.py
mutopia/model/model/model_components/_glm_compiled.py
mutopia/model/model/model_components/_hist_gbt.py
mutopia/model/model/model_components/_kmer_encoder.py
mutopia/model/model/model_components/_strand_transformer.py
mutopia/model/model/model_components/base.py
mutopia/model/model/model_components/context_model.py
mutopia/model/model/model_components/theta_model.py
mutopia/plot/__init__.py
mutopia/plot/bubble_plot.py
mutopia/plot/coef_matrix_plot.py
mutopia/plot/report.py
mutopia/plot/signature_plot.py
mutopia/plot/track_plot/__init__.py
mutopia/plot/track_plot/track_plot.py
mutopia/plot/track_plot/tracks.py
mutopia/plot/track_plot/transforms.py