.dockerignore
.gitignore
CLAUDE.md
DEVELOPING.md
Dockerfile
LICENSE
README.rst
pyproject.toml
setup.cfg
.github/workflows/docker.yml
.github/workflows/docs.yml
.github/workflows/publish.yml
.github/workflows/tests.yml
conda/README.md
conda/meta.yaml
encode_analysis/Makefile
encode_analysis/__init__.py
encode_analysis/base_config.yaml
encode_analysis/annotations/41588_2024_1659_MOESM5_ESM.xlsx
encode_analysis/annotations/at_gc_ratio.hg38.bed.gz
encode_analysis/annotations/blacklist_method12_v1_comb_sort_merged.bed.gz
encode_analysis/annotations/hg19ToHg38.over.chain.gz
encode_analysis/annotations/hg38.allchroms.txt
encode_analysis/annotations/hg38.cytoband.bed.gz
encode_analysis/annotations/hg38.mainchroms.sizes
encode_analysis/annotations/hg38.repeat_masker_fraction.bed.gz
encode_analysis/annotations/mutation-rate.hg38.bedgraph.gz
encode_analysis/annotations/replication-strand.hg38.bed.gz
encode_analysis/bin/aggregate-bed.sh
encode_analysis/bin/analysis_template.ipynb
encode_analysis/bin/extract-encode-gex.sh
encode_analysis/bin/merge-strand.sh
encode_analysis/bin/plot_summary.py
encode_analysis/bin/process-repliseq.sh
encode_analysis/bin/repeat-masker-fraction.sh
encode_analysis/bin/set_parameters.py
encode_analysis/bin/tile_genes.py
mutopia/__init__.py
mutopia/_version.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
tests/__init__.py
tests/build_chr22_fixture.py
tests/conftest.py
tests/test_cli.py
tests/test_gtensor_ops.py
tests/test_inference.py
tests/test_plotting.py
tests/test_training.py
tests/fixtures/.gitignore
website/Makefile
website/README.md
website/requirements.txt
website/.vscode/tasks.json
website/source/conf.py
website/source/getting_started.rst
website/source/index.rst
website/source/_static/custom.css
website/source/_static/gtensor_example.html
website/source/_static/mutopia_logo.png
website/source/api/gtensor.rst
website/source/api/index.rst
website/source/api/model.rst
website/source/api/plot.rst
website/source/api/modes/modes.rst
website/source/api/modes/sbs.rst
website/source/api/track_plot/track_plot.rst
website/source/api/track_plot/tracks.rst
website/source/api/track_plot/transforms.rst
website/source/tutorials/1.building_a_gtensor.ipynb
website/source/tutorials/2.analyzing_gtensors.ipynb
website/source/tutorials/3.training_models.ipynb
website/source/tutorials/4.analyzing_models.ipynb
website/source/tutorials/5.annotating_vcfs.rst
website/source/tutorials/6.genome_browser_plotting.ipynb
website/source/tutorials/index.rst