.gitignore
MANIFEST.in
PyMINEr_install.sh
PyMINEr_install_wo_dependencies.sh
README.md
TODO.txt
contributors.txt
installation_instructions.txt
requirements.txt
setup.py
bio_pyminer.egg-info/PKG-INFO
bio_pyminer.egg-info/SOURCES.txt
bio_pyminer.egg-info/dependency_links.txt
bio_pyminer.egg-info/requires.txt
bio_pyminer.egg-info/top_level.txt
docker/Dockerfile
docker/docker_notes.txt
example_usage/ID_list.txt
example_usage/adj_list_rho0.3.tsv
example_usage/adj_list_rho0.3_dedup.tsv
example_usage/adj_list_rho0.3_dedup_neg.tsv
example_usage/adj_list_rho0.3_dedup_pos.tsv
example_usage/how_to_use_PyMINEr_example.txt
example_usage/positive_negative_cor_counts.txt
example_usage/wine_dataset_clean_normalized.txt
example_usage/hdf5/ID_list.txt
example_usage/hdf5/adj_list_rho0.3.tsv
example_usage/hdf5/adj_list_rho0.3_dedup.tsv
example_usage/hdf5/adj_list_rho0.3_dedup_neg.tsv
example_usage/hdf5/adj_list_rho0.3_dedup_pos.tsv
example_usage/hdf5/column_IDs.txt
example_usage/hdf5/positive_negative_cor_counts.txt
example_usage/hdf5/wine_dataset_clean_normalized.hdf5
example_usage/hdf5/wine_dataset_clean_normalized.hdf5_copy
example_usage/hdf5/pos_cor_graphs/full_graph.png
example_usage/hdf5/pos_cor_graphs/full_graph_full.graphpkl
example_usage/hdf5/pos_cor_graphs/large_comps.graphpkl
example_usage/hdf5/pos_cor_graphs/sample_group_0.png
example_usage/hdf5/pos_cor_graphs/sample_group_1.png
example_usage/hdf5/rho_dicts/rho_0_to_13_vs_0_to_13.pkl
example_usage/hdf5/sample_clustering_and_summary/centroid_indices.txt
example_usage/hdf5/sample_clustering_and_summary/clustering_groups.png
example_usage/hdf5/sample_clustering_and_summary/f_lists_k_known.txt
example_usage/hdf5/sample_clustering_and_summary/f_lists_k_not_known.txt
example_usage/hdf5/sample_clustering_and_summary/k_group_enrichment.txt
example_usage/hdf5/sample_clustering_and_summary/k_group_means.txt
example_usage/hdf5/sample_clustering_and_summary/k_group_sd.txt
example_usage/hdf5/sample_clustering_and_summary/pca_projection.png
example_usage/hdf5/sample_clustering_and_summary/sample_k_means_groups.txt
example_usage/hdf5/sample_clustering_and_summary/tsne_projection.png
example_usage/hdf5/sample_clustering_and_summary/used_for_clustering_heatmap.png
example_usage/hdf5/sample_clustering_and_summary/significance/groups_1way_anova_results.txt
example_usage/hdf5/sample_clustering_and_summary/significance/number_of_variables_significant_and_enriched_for_each_group.txt
example_usage/hdf5/sample_clustering_and_summary/significance/sample_group_0_significant_enriched.txt
example_usage/hdf5/sample_clustering_and_summary/significance/sample_group_1_significant_enriched.txt
example_usage/hdf5/sample_clustering_and_summary/significance/significant_and_enriched_boolean_table.txt
example_usage/pos_cor_graphs/full_graph.png
example_usage/pos_cor_graphs/full_graph_full.graphpkl
example_usage/pos_cor_graphs/large_comps.graphpkl
example_usage/pos_cor_graphs/sample_group_0.png
example_usage/pos_cor_graphs/sample_group_1.png
example_usage/rho_dicts/rho_0_to_13_vs_0_to_13.pkl
example_usage/sample_clustering_and_summary/centroid_indices.txt
example_usage/sample_clustering_and_summary/clustering_groups.png
example_usage/sample_clustering_and_summary/f_lists_k_known.txt
example_usage/sample_clustering_and_summary/f_lists_k_not_known.txt
example_usage/sample_clustering_and_summary/k_group_enrichment.txt
example_usage/sample_clustering_and_summary/k_group_means.txt
example_usage/sample_clustering_and_summary/k_group_sd.txt
example_usage/sample_clustering_and_summary/pca_projection.png
example_usage/sample_clustering_and_summary/sample_k_means_groups.txt
example_usage/sample_clustering_and_summary/sample_var_enrichment_Zscores.txt
example_usage/sample_clustering_and_summary/tsne_projection.png
example_usage/sample_clustering_and_summary/used_for_clustering_heatmap.png
example_usage/sample_clustering_and_summary/significance/groups_1way_anova_results.txt
example_usage/sample_clustering_and_summary/significance/number_of_variables_significant_and_enriched_for_each_group.txt
example_usage/sample_clustering_and_summary/significance/sample_group_0_significant_enriched.txt
example_usage/sample_clustering_and_summary/significance/sample_group_1_significant_enriched.txt
example_usage/sample_clustering_and_summary/significance/significant_and_enriched_boolean_table.txt
lib/10090.protein.actions.v11.0.txt.gz
lib/9606.protein.actions.v11.0.txt.gz
lib/PanglaoDB_markers_25_Nov_2019.tsv.gz
lib/PanglaoDB_markers_25_Nov_2019.xls
lib/all_cell_markers.txt.gz
lib/all_cell_markers_reorg.xls
lib/chip_tad_boundaries_hg38.bed
lib/chip_tad_boundaries_hg38.bed.gz
lib/gene_contig_loci.tsv
lib/tad_dict.pkl
lib/unified_technical_mmusculus_chromium_v3.tsv
pyminer/10090.protein.actions.v11.0.txt
pyminer/9606.protein.actions.v11.0.txt
pyminer/__init__.py
pyminer/cell_signals.py
pyminer/clustering.py
pyminer/combine_gprofiler_results.py
pyminer/common_functions.py
pyminer/get_degrees_of_separation_from_adjacency_list.py
pyminer/get_high_marker_genes.py
pyminer/get_stats.py
pyminer/make_website.py
pyminer/mat_to_adj_list.py
pyminer/plot_gene_subset.py
pyminer/plot_network.py
pyminer/pyminer.py
pyminer/pyminer_analyze_communities.py
pyminer/pyminer_analyze_pathologic_genes.py
pyminer/pyminer_annotate_variants_to_genes.py
pyminer/pyminer_bayes.py
pyminer/pyminer_cell_graph_plotting.py
pyminer/pyminer_clust_funcs.py
pyminer/pyminer_common_stats_functions.py
pyminer/pyminer_continuous_lineage_pseudotime.py
pyminer/pyminer_convert_to_scanpy.py
pyminer/pyminer_ensembl_rest.py
pyminer/pyminer_feature_selection.py
pyminer/pyminer_gene_term_comentions.py
pyminer/pyminer_get_dispersion.py
pyminer/pyminer_get_stats.py
pyminer/pyminer_global_test.py
pyminer/pyminer_gprofile.py
pyminer/pyminer_gprofiler_converter.py
pyminer/pyminer_h5_to_tab.py
pyminer/pyminer_objs.py
pyminer/pyminer_process_tad_bed.py
pyminer/pyminer_recursive_clust.py
pyminer/pyminer_tm_norm.py
pyminer/tab_to_h5.py
pyminer/unified_technical_mmusculus_chromium_v3.tsv
pyminer/unified_technical_mmusculus_chromium_v3.tsv.gz
pyminer/__pycache__/__init__.cpython-37.pyc
pyminer/__pycache__/get_stats.cpython-37.pyc
pyminer/__pycache__/pyminer_annotate_variants_to_genes.cpython-37.pyc
pyminer/__pycache__/pyminer_ensembl_rest.cpython-37.pyc
pyminer/__pycache__/pyminer_gene_term_comentions.cpython-37.pyc
pyminer/__pycache__/pyminer_gprofiler_converter.cpython-37.pyc
pyminer/__pycache__/pyminer_process_tad_bed.cpython-37.pyc
pyminer/aux/LPR_correlation_assessment.py
pyminer/aux/LPR_dataset_reconstruction.py
pyminer/aux/adj_to_ensg_adj.py
pyminer/aux/collate_multiple_enrichment_lists.py
pyminer/aux/combine_multiple_adj_lists.py
pyminer/aux/compare_shortest_path_mats.py
pyminer/aux/find_doublets.py
pyminer/aux/get_max_shortest_path.py
pyminer/aux/get_within_group_disperssion.py
pyminer/aux/lineage_analysis.py
pyminer/aux/map_table_to_ensg.py
pyminer/aux/pyminer_annotate_cell_types.py
pyminer/aux/pyminer_chi_res.py
pyminer/aux/pyminer_class_lineage_effects.py
pyminer/aux/pyminer_do_class_analyses.py
pyminer/aux/pyminer_get_binary_expression_lists.py
pyminer/aux/pyminer_get_lincs.py
pyminer/aux/pyminer_make_cont_table.py
pyminer/aux/pyminer_polygenic_complex_scores.py
pyminer/aux/pyminer_process_cell_marker_dbs.py
pyminer/aux/pyminer_proportionality_statistic.py
pyminer/aux/pyminer_short_key_driver.py
pyminer/aux/pyminer_within_group_differences.py
pyminer/aux/subset_adj_list.py
pyminer/aux/unify_datasets.py
pyminer/aux/__pycache__/lineage_analysis.cpython-37.pyc
pyminer/aux/__pycache__/pyminer_analyze_catelogue.cpython-37.pyc
pyminer/legacy/MINE.jar
pyminer/legacy/PyMINEr_5.19.py
pyminer/legacy/PyMINEr_6.00.py
pyminer/legacy/PyMINEr_pipeline_1.02.py
pyminer/legacy/create_within_group_boot_1.01.py
pyminer/legacy/install_cell_signals.sh
pyminer/legacy/make_FPR_curve_1.4.py
pyminer/legacy/mine_R_cutoff_filter.py
pyminer/legacy/old_PyMINEr_install.sh
pyminer/legacy/old_combine_gprofiler_results.py
pyminer/legacy/remove_dups.py
pyminer/legacy/web/app.py
pyminer/legacy/web/requirements.txt
pyminer/legacy/web/static/css/main.css
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap-theme.css
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap-theme.css.map
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap-theme.min.css
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap-theme.min.css.map
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap.css
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap.css.map
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap.min.css
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/bootstrap.min.css.map
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/css/ie10-viewport-bug-workaround.css
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/fonts/glyphicons-halflings-regular.eot
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/fonts/glyphicons-halflings-regular.svg
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/fonts/glyphicons-halflings-regular.ttf
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/fonts/glyphicons-halflings-regular.woff
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/fonts/glyphicons-halflings-regular.woff2
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/js/bootstrap.js
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/js/bootstrap.min.js
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/js/ie10-viewport-bug-workaround.js
pyminer/legacy/web/static/vendor/bootstrap-3.3.7/js/npm.js
pyminer/legacy/web/static/vendor/jquery/jquery-3.1.0.min.js
pyminer/legacy/web/templates/about.html
pyminer/legacy/web/templates/contact.html
pyminer/legacy/web/templates/index.html
pyminer/legacy/web/templates/layout.html
pyminer/legacy/web/templates/status.html