LICENSE.md
MANIFEST.in
README.md
setup.cfg
setup.py
src/pytpp/__init__.py
src/pytpp/__main__.py
src/pytpp/tpp_gui.py
src/pytpp/tpp_tools.py
src/pytpp/tpp_tools_regex.py
src/pytransit/__init__.py
src/pytransit/__main__.py
src/pytransit/draw_trash.py
src/pytransit/fileDisplay.py
src/pytransit/images.py
src/pytransit/norm_tools.py
src/pytransit/qcDisplay.py
src/pytransit/stat_tools.py
src/pytransit/tnseq_tools.py
src/pytransit/tnseq_tools_corrections.py
src/pytransit/transit_gui.py
src/pytransit/transit_tools.py
src/pytransit/trash.py
src/pytransit/view_trash.py
src/pytransit/analysis/__init__.py
src/pytransit/analysis/anova.py
src/pytransit/analysis/base.py
src/pytransit/analysis/binomial.py
src/pytransit/analysis/corrplot.py
src/pytransit/analysis/essentiality.py
src/pytransit/analysis/example.py
src/pytransit/analysis/extract_GO_term_names.py
src/pytransit/analysis/extract_sanger.py
src/pytransit/analysis/gi.py
src/pytransit/analysis/griffin.py
src/pytransit/analysis/gumbel.py
src/pytransit/analysis/gumbel_mod.py
src/pytransit/analysis/gumbel_mod2.py
src/pytransit/analysis/gumbel_mod3.py
src/pytransit/analysis/gumbel_orig.py
src/pytransit/analysis/heatmap.py
src/pytransit/analysis/hmm.py
src/pytransit/analysis/norm.py
src/pytransit/analysis/normalize.py
src/pytransit/analysis/pathway_enrichment.py
src/pytransit/analysis/rankproduct.py
src/pytransit/analysis/resampling.py
src/pytransit/analysis/resampling_mod.py
src/pytransit/analysis/temp-gi.py
src/pytransit/analysis/temp.py
src/pytransit/analysis/temp1.py
src/pytransit/analysis/tn5gaps.py
src/pytransit/analysis/tnseq_stats.py
src/pytransit/analysis/utest.py
src/pytransit/analysis/zinb-interac.py
src/pytransit/analysis/zinb.py
src/pytransit/analysis/tmp/__init__.py
src/pytransit/analysis/tmp/anova.py
src/pytransit/analysis/tmp/base.py
src/pytransit/analysis/tmp/binomial.py
src/pytransit/analysis/tmp/corrplot.py
src/pytransit/analysis/tmp/essentiality.py
src/pytransit/analysis/tmp/example.py
src/pytransit/analysis/tmp/extract_GO_term_names.py
src/pytransit/analysis/tmp/extract_sanger.py
src/pytransit/analysis/tmp/gi.py
src/pytransit/analysis/tmp/griffin.py
src/pytransit/analysis/tmp/gumbel.py
src/pytransit/analysis/tmp/gumbel_mod.py
src/pytransit/analysis/tmp/gumbel_mod2.py
src/pytransit/analysis/tmp/gumbel_mod3.py
src/pytransit/analysis/tmp/gumbel_orig.py
src/pytransit/analysis/tmp/heatmap.py
src/pytransit/analysis/tmp/hmm.py
src/pytransit/analysis/tmp/norm.py
src/pytransit/analysis/tmp/normalize.py
src/pytransit/analysis/tmp/pathway_enrichment.py
src/pytransit/analysis/tmp/rankproduct.py
src/pytransit/analysis/tmp/resampling.py
src/pytransit/analysis/tmp/resampling_mod.py
src/pytransit/analysis/tmp/temp-gi.py
src/pytransit/analysis/tmp/temp1.py
src/pytransit/analysis/tmp/tn5gaps.py
src/pytransit/analysis/tmp/tnseq_stats.py
src/pytransit/analysis/tmp/utest.py
src/pytransit/analysis/tmp/zinb-interac.py
src/pytransit/analysis/tmp/zinb.py
src/pytransit/convert/__init__.py
src/pytransit/convert/base.py
src/pytransit/convert/gff_to_prot_table.py
src/pytransit/data/COG_roles.dat
src/pytransit/data/GO_associated_Rvs-3-11-18.txt
src/pytransit/data/GO_associated_Rvs.csv
src/pytransit/data/GO_term_names.dat
src/pytransit/data/GO_terms_for_each_Rv.obo-3-11-18.txt
src/pytransit/data/H37Rv.sanger_associated_RVS.csv
src/pytransit/data/H37Rv_COG_roles.dat
src/pytransit/data/H37Rv_GO_terms.txt
src/pytransit/data/H37Rv_sanger_roles.dat
src/pytransit/data/README.md
src/pytransit/data/README.md~
src/pytransit/data/cholesterol_H37Rv_merged.wig
src/pytransit/data/cholesterol_H37Rv_rep1.wig
src/pytransit/data/cholesterol_H37Rv_rep2.wig
src/pytransit/data/cholesterol_H37Rv_rep3.wig
src/pytransit/data/cholesterol_glycerol_combined.dat
src/pytransit/data/count_GO_terms.py
src/pytransit/data/count_GO_terms.py~
src/pytransit/data/gene_ontology.1_2.3-11-18.obo
src/pytransit/data/glycerol_H37Rv_merged.wig
src/pytransit/data/glycerol_H37Rv_rep1.wig
src/pytransit/data/glycerol_H37Rv_rep2.wig
src/pytransit/data/iron_related_GO_terms.txt
src/pytransit/data/list_GO_terms.py
src/pytransit/data/list_GO_terms.py~
src/pytransit/data/samples_metadata_cg.txt
src/pytransit/data/samples_metadata_cg_covar.txt
src/pytransit/data/samples_metadata_cg_interactions.txt
src/pytransit/data/sanger_roles.dat
src/pytransit/data/smeg_GO_terms.txt
src/pytransit/doc/build/html/genindex.html
src/pytransit/doc/build/html/index.html
src/pytransit/doc/build/html/py-modindex.html
src/pytransit/doc/build/html/pytransit.analysis.html
src/pytransit/doc/build/html/pytransit.html
src/pytransit/doc/build/html/search.html
src/pytransit/doc/build/html/tpp.html
src/pytransit/doc/build/html/transit.html
src/pytransit/doc/build/html/transit_console_cheatsheet.html
src/pytransit/doc/build/html/transit_export_tutorial.html
src/pytransit/doc/build/html/transit_features.html
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src/pytransit/doc/build/html/transit_interactions_tutorial.html
src/pytransit/doc/build/html/transit_methods.html
src/pytransit/doc/build/html/transit_normalization_tutorial.html
src/pytransit/doc/build/html/transit_overview.html
src/pytransit/doc/build/html/transit_running.html
src/pytransit/doc/build/html/_images/TPP-screenshot.png
src/pytransit/doc/build/html/_images/genetic_interaction_types.png
src/pytransit/doc/build/html/_images/glyc_chol_corrplot.png
src/pytransit/doc/build/html/_images/iron_corrplot_anova.png
src/pytransit/doc/build/html/_images/iron_heatmap_anova_rotated.png
src/pytransit/doc/build/html/_images/transit_dataset_scatter_graph.png
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src/pytransit/doc/build/html/_images/transit_interface.png
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src/pytransit/doc/build/html/_images/transit_quality_control_qqplot.png
src/pytransit/doc/build/html/_images/transit_quality_control_ranked.png
src/pytransit/doc/build/html/_images/transit_quality_control_window.png
src/pytransit/doc/build/html/_images/transit_resampling_histogram_graph.png
src/pytransit/doc/build/html/_images/transit_result_volcano_graph.png
src/pytransit/doc/build/html/_images/transit_tutorial_annotation.png
src/pytransit/doc/build/html/_images/transit_tutorial_control_datasets.png
src/pytransit/doc/build/html/_images/transit_tutorial_gi_control_A.png
src/pytransit/doc/build/html/_images/transit_tutorial_gi_control_B.png
src/pytransit/doc/build/html/_images/transit_tutorial_gi_experimental_A.png
src/pytransit/doc/build/html/_images/transit_tutorial_gi_experimental_B.png
src/pytransit/doc/build/html/_images/transit_tutorial_gi_method.png
src/pytransit/doc/build/html/_images/transit_tutorial_norm_options.png
src/pytransit/doc/build/html/_modules/index.html
src/pytransit/doc/build/html/_modules/pytransit/draw_trash.html
src/pytransit/doc/build/html/_modules/pytransit/fileDisplay.html
src/pytransit/doc/build/html/_modules/pytransit/norm_tools.html
src/pytransit/doc/build/html/_modules/pytransit/qcDisplay.html
src/pytransit/doc/build/html/_modules/pytransit/stat_tools.html
src/pytransit/doc/build/html/_modules/pytransit/tnseq_tools.html
src/pytransit/doc/build/html/_modules/pytransit/transit_gui.html
src/pytransit/doc/build/html/_modules/pytransit/transit_tools.html
src/pytransit/doc/build/html/_modules/pytransit/trash.html
src/pytransit/doc/build/html/_modules/pytransit/view_trash.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/anova.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/base.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/binomial.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/example.html
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src/pytransit/doc/build/html/_modules/pytransit/analysis/hmm.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/rankproduct.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/resampling.html
src/pytransit/doc/build/html/_modules/pytransit/analysis/tn5gaps.html
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src/pytransit/doc/build/html/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2
src/pytransit/doc/build/html/_static/js/badge_only.js
src/pytransit/doc/build/html/_static/js/html5shiv-printshiv.min.js
src/pytransit/doc/build/html/_static/js/html5shiv.min.js
src/pytransit/doc/build/html/_static/js/modernizr.min.js
src/pytransit/doc/build/html/_static/js/theme.js
src/pytransit/export/__init__.py
src/pytransit/export/base.py
src/pytransit/export/combined_wig.py
src/pytransit/export/igv.py
src/pytransit/export/mean_counts.py
src/pytransit/export/prot_table.py
src/pytransit/genomes/BCG.fna
src/pytransit/genomes/BCG.prot_table
src/pytransit/genomes/H37Rv.fna
src/pytransit/genomes/H37Rv.fna.amb
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src/pytransit/genomes/H37Rv.fna.bwt
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src/pytransit/genomes/H37RvBD_mod3.prot_table
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src/pytransit/genomes/genomes.html~
src/pytransit/genomes/mc2_155_tamu.fna
src/pytransit/genomes/mc2_155_tamu.prot_table
tnseq_transit.egg-info/PKG-INFO
tnseq_transit.egg-info/SOURCES.txt
tnseq_transit.egg-info/dependency_links.txt
tnseq_transit.egg-info/entry_points.txt
tnseq_transit.egg-info/requires.txt
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