LICENSE
README.rst
setup.py
databases/hybkit_coding_ref_combined.csv
databases/hybkit_coding_ref_combined.notes.txt
docs/Makefile
docs/conf.py
docs/docs_readme_format.rst
docs/index.rst
docs/make.bat
docs/requirements.txt
docs/sample_01_link.rst
docs/sample_02_link.rst
docs/sample_03_link.rst
docs/sample_04_link.rst
docs/sample_05_link.rst
docs/source/about.rst
docs/source/example_pipelines.rst
docs/source/hybkit.analysis.rst
docs/source/hybkit.plot.rst
docs/source/hybkit.rst
docs/source/hybkit.util.rst
docs/source/hybkit_api.rst
docs/source/hybkit_toolkit.rst
docs/source/specification.rst
docs/source/toolkit/hyb_analysis.rst
docs/source/toolkit/hyb_check.rst
docs/source/toolkit/hyb_filter.rst
hybkit/__about__.py
hybkit/__about__.pyc
hybkit/__init__.py
hybkit/__init__.pyc
hybkit/analysis.py
hybkit/analysis.pyc
hybkit/plot.py
hybkit/string_match_params.csv
hybkit/util.py
hybkit.egg-info/PKG-INFO
hybkit.egg-info/SOURCES.txt
hybkit.egg-info/dependency_links.txt
hybkit.egg-info/requires.txt
hybkit.egg-info/top_level.txt
reference_data/WT_BR1_comp_hOH7_KSHV_hybrids_ua.hyb.gz
reference_data/WT_BR1_comp_hOH7_KSHV_hybrids_ua.viennad.gz
sample_01_summary_analysis/analysis_python.py
sample_01_summary_analysis/download_data.sh
sample_01_summary_analysis/string_match_legend.csv
sample_01_summary_analysis/summary_analysis_notes.rst
sample_02_target_analysis/analysis_python.py
sample_02_target_analysis/download_data.sh
sample_02_target_analysis/string_match_legend.csv
sample_02_target_analysis/target_analysis_notes.rst
sample_03_grouped_target_analysis/analysis_python.py
sample_03_grouped_target_analysis/download_data.sh
sample_03_grouped_target_analysis/grouped_target_analysis_notes.rst
sample_03_grouped_target_analysis/string_match_legend.csv
sample_04_fold_analysis/analysis_python.py
sample_04_fold_analysis/fold_analysis_notes.rst
sample_04_fold_analysis/prepare_data.sh
sample_04_fold_analysis/string_match_legend.csv
sample_05_fold_target_region_analysis/analysis_python.py
sample_05_fold_target_region_analysis/fold_target_region_notes.rst
sample_05_fold_target_region_analysis/prepare_data.sh
sample_05_fold_target_region_analysis/string_match_legend.csv
scripts/hyb_analysis
scripts/hyb_check
scripts/hyb_filter
scripts/hyb_type_analysis
scripts_extra/biomart_coding_ref_archive.py
scripts_extra/biomart_coding_ref_archive.py.deprecated
scripts_extra/biomart_coding_ref_to_hybkit.py