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.gitignore
.travis.yml
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
README.rst
environment.yml
nbval_sanitize.cfg
pytest.ini
setup.py
test_requirements.txt
dms_variants/__init__.py
dms_variants/_cutils.c
dms_variants/barcodes.py
dms_variants/binarymap.py
dms_variants/bottlenecks.py
dms_variants/codonvarianttable.py
dms_variants/constants.py
dms_variants/fastq.py
dms_variants/globalepistasis.py
dms_variants/illuminabarcodeparser.py
dms_variants/ispline.py
dms_variants/pdb_utils.py
dms_variants/plotnine_themes.py
dms_variants/simulate.py
dms_variants/utils.py
dms_variants.egg-info/PKG-INFO
dms_variants.egg-info/SOURCES.txt
dms_variants.egg-info/dependency_links.txt
dms_variants.egg-info/requires.txt
dms_variants.egg-info/top_level.txt
docs/.nojekyll
docs/Makefile
docs/README.rst
docs/acknowledgments.rst
docs/bottleneck_likelihood.nblink
docs/codonvariant_plot_formatting.nblink
docs/codonvariant_sim_data.nblink
docs/codonvariant_sim_data_multi_targets.nblink
docs/conf.py
docs/doc_requirements.txt
docs/examples.rst
docs/index.rst
docs/installation.rst
docs/narrow_bottleneck.nblink
docs/package_index.rst
docs/parsebarcodes_sim_data.nblink
docs/_static/BloomLogo.jpg
notebooks/README.rst
notebooks/bottleneck_likelihood.ipynb
notebooks/codonvariant_plot_formatting.ipynb
notebooks/codonvariant_sim_data.ipynb
notebooks/codonvariant_sim_data_multi_targets.ipynb
notebooks/multi_latent_phenos.ipynb
notebooks/narrow_bottleneck.ipynb
notebooks/parsebarcodes_sim_data.ipynb
notebooks/predict_variants.ipynb
tests/.gitignore
tests/README.rst
tests/bottleneck_likelihood_deriv_equations.ipynb
tests/codonvarianttable_toy_example.ipynb
tests/epistasis_model_preferences.ipynb
tests/illuminabarcodeparser_toy_example.ipynb
tests/monotonicsplineepistasisbottlenecklikelihood_model.ipynb
tests/monotonicsplineepistasiscauchylikelihood_model.ipynb
tests/monotonicsplineepistasisgaussianlikelihood_model.ipynb
tests/noepistasisbottlenecklikelihood_model.ipynb
tests/noepistasisgaussianlikelihood_model.ipynb
tests/test_count_codonvariants.py
tests/test_escape_scores.ipynb
tests/count_codonvariant_files/PacBio_amplicon.gb
tests/count_codonvariant_files/barcode_variant_table.csv
tests/count_codonvariant_files/fates.csv
tests/count_codonvariant_files/library-1_plasmid_R1.fastq
tests/count_codonvariant_files/library-1_plasmid_R2.fastq
tests/count_codonvariant_files/library-1_uninduced_R1.fastq
tests/count_codonvariant_files/library-1_uninduced_R2.fastq
tests/count_codonvariant_files/library-2_plasmid_R1.fastq
tests/count_codonvariant_files/library-2_plasmid_R2.fastq
tests/count_codonvariant_files/n_variants.csv
tests/count_codonvariant_files/variant_counts.csv