├── .dockerignore ├── .gitignore ├── .travis.yml ├── Dockerfile ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── cmapPy ├── __init__.py ├── clue_api_client │ ├── __init__.py │ ├── cell_queries.py │ ├── clue_api_client.py │ ├── gene_queries.py │ ├── macchiato_queries.py │ ├── mock_clue_api_client.py │ ├── pert_queries.py │ ├── setup_logger.py │ └── tests │ │ ├── test_cell_queries.py │ │ ├── test_clue_api_client.py │ │ ├── test_gene_queries.py │ │ ├── test_macchiato_queries.py │ │ ├── test_mock_clue_api_client.py │ │ └── test_pert_queries.py ├── example_cmapPy_config_file.cfg ├── math │ ├── __init__.py │ ├── agg_wt_avg.py │ ├── fast_corr.py │ ├── fast_cov.py │ ├── robust_zscore.py │ └── tests │ │ ├── __init__.py │ │ ├── test_agg_wt_avg.py │ │ ├── test_fast_corr.py │ │ ├── test_fast_cov.py │ │ └── test_robust_zscore.py ├── pandasGEXpress │ ├── GCToo.py │ ├── README.rst │ ├── __init__.py │ ├── concat.py │ ├── concat_gctoo.py │ ├── diff_gctoo.py │ ├── gct2gctx.py │ ├── gctx2gct.py │ ├── mini_gctoo_for_testing.py │ ├── parse.py │ ├── parse_gct.py │ ├── parse_gctx.py │ ├── random_slice.py │ ├── setup_GCToo_logger.py │ ├── simple_GCT_to_GCToo_figure.png │ ├── slice_gct.py │ ├── slice_gctoo.py │ ├── subset.py │ ├── subset_gctoo.py │ ├── tests │ │ ├── __init__.py │ │ ├── functional_tests │ │ │ ├── LJP_row_metadata.txt │ │ │ ├── both_metadata_example_n1476x978.gct │ │ │ ├── both_metadata_example_n1476x978.gctx │ │ │ ├── col_meta_only_example_n355x355.gct │ │ │ ├── col_meta_only_example_n355x355.gctx │ │ │ ├── concated.gctx │ │ │ ├── metadata_writer_test.gctx │ │ │ ├── mini_folder │ │ │ │ ├── both_metadata_example_n1476x978.gctx │ │ │ │ ├── col_meta_only_example_n355x355.gctx │ │ │ │ ├── row_meta_only_example_n2x1203.gctx │ │ │ │ └── tsne_n2x1203.gctx │ │ │ ├── mini_gctoo_data_matrix.gctx │ │ │ ├── mini_gctoo_for_testing.gct │ │ │ ├── mini_gctoo_for_testing.gctx │ │ │ ├── mini_gctoo_for_testing_nometa.gct │ │ │ ├── mini_gctoo_for_testing_nometa.gctx │ │ │ ├── mini_gctx_with_metadata_n2x3.gctx │ │ │ ├── older_version_v1_2.gct │ │ │ ├── row_meta_only_example_n2x1203.gct │ │ │ ├── row_meta_only_example_n2x1203.gctx │ │ │ ├── test_colmeta_n6.txt │ │ │ ├── test_concat │ │ │ │ └── test_main │ │ │ │ │ ├── a.gct │ │ │ │ │ └── b.gct │ │ │ ├── test_concat_gctoo_test_main_fake_empty_file.gct │ │ │ ├── test_l1000.gct │ │ │ ├── test_l1000.gctx │ │ │ ├── test_l1000_highprecision.gct │ │ │ ├── test_l1000_highprecision.gctx │ │ │ ├── test_merge_bottom.gct │ │ │ ├── test_merge_left.gct │ │ │ ├── test_merge_right.gct │ │ │ ├── test_merge_top.gct │ │ │ ├── test_merged_left_right.gct │ │ │ ├── test_merged_top_bottom.gct │ │ │ ├── test_missing_colmeta.txt │ │ │ ├── test_missing_rowmeta.txt │ │ │ ├── test_p100.gct │ │ │ ├── test_parse_gct_int_ids.gct │ │ │ ├── test_parse_gctx_rid_entrez_id.gctx │ │ │ ├── test_rowmeta_n6.txt │ │ │ ├── test_subset_expected.gct │ │ │ ├── test_subset_in.gct │ │ │ ├── test_subset_rid.grp │ │ │ ├── test_v1point2_n5x10.gct │ │ │ └── tsne_n2x1203.gctx │ │ ├── python2_tests │ │ │ ├── __init__.py │ │ │ ├── test_GCToo.py │ │ │ ├── test_concat.py │ │ │ ├── test_diff_gctoo.py │ │ │ ├── test_edge_cases.py │ │ │ ├── test_gct2gctx.py │ │ │ ├── test_gctx2gct.py │ │ │ ├── test_parse.py │ │ │ ├── test_parse_gct.py │ │ │ ├── test_parse_gctx.py │ │ │ ├── test_random_slice.py │ │ │ ├── test_subset.py │ │ │ ├── test_subset_gctoo.py │ │ │ ├── test_write_gct.py │ │ │ └── test_write_gctx.py │ │ ├── python3_tests │ │ │ ├── __init__.py │ │ │ ├── test_GCToo.py │ │ │ ├── test_concat.py │ │ │ ├── test_diff_gctoo.py │ │ │ ├── test_edge_cases.py │ │ │ ├── test_gct2gctx.py │ │ │ ├── test_gctx2gct.py │ │ │ ├── test_parse.py │ │ │ ├── test_parse_gct.py │ │ │ ├── test_parse_gctx.py │ │ │ ├── test_random_slice.py │ │ │ ├── test_subset.py │ │ │ ├── test_subset_gctoo.py │ │ │ ├── test_transform_gctoo.py │ │ │ ├── test_write_gct.py │ │ │ └── test_write_gctx.py │ │ └── test_python2_python3_compatibility.py │ ├── transform_gctoo.py │ ├── write_gct.py │ └── write_gctx.py ├── set_io │ ├── __init__.py │ ├── gmt.py │ ├── grp.py │ └── tests │ │ ├── __init__.py │ │ ├── functional_tests │ │ ├── test.gmt │ │ ├── test.grp │ │ ├── test_bad.gmt │ │ └── test_bad2.gmt │ │ ├── test_gmt.py │ │ └── test_grp.py └── visualization │ ├── .gitignore │ ├── __init__.py │ ├── cohort_view.py │ ├── scattergram.py │ ├── stratogram.py │ ├── test_cohort_view.py │ ├── test_files │ └── PBRANT_CYCLE1_key_metrics_expanded_sample.txt │ ├── test_scattergram.py │ └── test_stratogram.py ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── available_modules.rst │ ├── build.rst │ ├── citing.rst │ ├── clue_api_client.rst │ ├── conf.py │ ├── contributing.rst │ ├── faq.rst │ ├── index.rst │ ├── licenses.rst │ ├── pandasGEXpress.rst │ ├── pandasgexpress_fig.png │ └── set_io.rst ├── nginx.conf ├── performance_testing ├── python_parse_timing.py └── python_write_timing.py ├── requirements.txt ├── setup.cfg ├── setup.py └── tutorials ├── 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