MANIFEST.in
README.md
setup.py
CountESS.egg-info/PKG-INFO
CountESS.egg-info/SOURCES.txt
CountESS.egg-info/dependency_links.txt
CountESS.egg-info/entry_points.txt
CountESS.egg-info/requires.txt
CountESS.egg-info/top_level.txt
countess/__init__.py
countess/main.py
countess/base/__init__.py
countess/base/config_constants.py
countess/base/constants.py
countess/base/dataframe.py
countess/base/storemanager.py
countess/base/utils.py
countess/config/__init__.py
countess/config/config_check.py
countess/config/types.py
countess/experiment/__init__.py
countess/experiment/condition.py
countess/experiment/experiment.py
countess/gui/__init__.py
countess/gui/configurator.py
countess/gui/create_root_dialog.py
countess/gui/create_seqlib_dialog.py
countess/gui/delete_dialog.py
countess/gui/dialog.py
countess/gui/dialog_elements.py
countess/gui/edit_dialog.py
countess/gui/logging_frame.py
countess/gui/options_frame.py
countess/gui/plugin.py
countess/gui/plugin_source_window.py
countess/gui/seqlib_apply_dialog.py
countess/libraries/__init__.py
countess/libraries/barcode.py
countess/libraries/barcodeid.py
countess/libraries/barcodemap.py
countess/libraries/barcodevariant.py
countess/libraries/basic.py
countess/libraries/idonly.py
countess/libraries/seqlib.py
countess/libraries/variant.py
countess/plugins/__init__.py
countess/plugins/options.py
countess/plugins/scoring.py
countess/selection/__init__.py
countess/selection/selection.py
countess/sequence/__init__.py
countess/sequence/aligner.py
countess/sequence/fqread.py
countess/sequence/wildtype.py
countess/statistics/__init__.py
countess/statistics/random_effects.py
countess/statistics/ztest.py
countess/store/__init__.py
countess/store/csv.py
countess/store/hdf.py
countess/store/interface.py
countess/store/parquet.py
countess/tests/__init__.py
countess/tests/methods.py
countess/tests/test_enrich2.py
countess/tests/test_experiment_barcode_lib.py
countess/tests/test_experiment_barcodeid_lib.py
countess/tests/test_experiment_barcodevariant_lib_coding.py
countess/tests/test_experiment_barcodevariant_lib_noncoding.py
countess/tests/test_experiment_basic_lib_coding.py
countess/tests/test_experiment_basic_lib_noncoding.py
countess/tests/test_experiment_idonly_lib.py
countess/tests/test_lib_barcode.py
countess/tests/test_lib_barcodeid.py
countess/tests/test_lib_barcodevariant_coding.py
countess/tests/test_lib_barcodevariant_noncoding.py
countess/tests/test_lib_basic_coding.py
countess/tests/test_lib_basic_noncoding.py
countess/tests/test_lib_idonly.py
countess/tests/test_module_ambivert_aligner.py
countess/tests/test_module_config_check.py
countess/tests/test_module_config_types.py
countess/tests/test_module_dataframe.py
countess/tests/test_module_enrich2_aligner.py
countess/tests/test_module_fqreader.py
countess/tests/test_module_options.py
countess/tests/test_module_plugins_base.py
countess/tests/test_module_types_basic.py
countess/tests/test_module_types_libs.py
countess/tests/test_module_types_sel_exp_cond.py
countess/tests/test_module_variant.py
countess/tests/test_module_wildtype.py
countess/tests/test_selection_barcode_lib.py
countess/tests/test_selection_barcodeid_lib.py
countess/tests/test_selection_barcodevariant_lib_coding.py
countess/tests/test_selection_barcodevariant_lib_noncoding.py
countess/tests/test_selection_basic_lib_coding.py
countess/tests/test_selection_basic_lib_noncoding.py
countess/tests/test_selection_idonly_lib.py
countess/tests/test_selection_timepoint_merge.py
countess/tests/test_selection_valueerrors.py
countess/tests/utilities.py
docs/Makefile
docs/api.rst
docs/conf.py
docs/gui.rst
docs/index.rst
docs/installation.rst
docs/introduction.rst
docs/make.bat
docs/notebooks.rst
docs/output.rst
docs/plots.rst
docs/scripting.rst
docs/seqlib_config.rst
docs/_static/iD_icon.png
docs/_static/cartoons/data_hierarchy.png
docs/_static/cartoons/overlap.png
docs/_static/cartoons/overlap_reads.png
docs/_static/gui_screenshots/complete_example.png
docs/_static/gui_screenshots/context_menu.png
docs/_static/gui_screenshots/empty.png
docs/_static/gui_screenshots/new_child.png
docs/_static/gui_screenshots/new_root.png
docs/_static/gui_screenshots/seqlib.png
docs/_static/gui_screenshots/seqlib_choice.png
docs/_static/notebook_plots/min_count_plot.png
docs/_static/notebook_plots/unique_barcodes_plot.png
docs/_static/plots/barcodes_per_variant.png
docs/_static/plots/diversity.png
docs/_static/plots/overlap_mismatches.png
docs/_static/plots/regression_weights.png
docs/_static/plots/se_pctile.png
docs/_static/plots/selection_counts.png
docs/_static/plots/seqlib_counts.png
docs/_static/plots/sfmap.png
docs/_static/plots/volcano.png
docs/_static/plots/wt_shape.png
docs/exported_notebooks/README
docs/exported_notebooks/min_count.rst
docs/exported_notebooks/unique_barcodes.rst
docs/notebooks/min_count.ipynb
docs/notebooks/unique_barcodes.ipynb
tests/__init__.py
tests/test_store/__init__.py
tests/test_store/store_interface_tests.py
tests/test_store/test_store_csv.py
tests/test_store/test_store_hdf.py
tests/test_store/test_store_parquet.py