├── .gitignore ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── about_ccmap_file.rst ├── about_gcmap_file.rst ├── about_h5_file.rst ├── apidoc │ ├── ccmap.rst │ ├── ccmapHelpers.rst │ ├── cmstats.rst │ ├── config.rst │ ├── corrMatrix.rst │ ├── gcmap.rst │ ├── genomicsDataHandler │ │ ├── EncodeDatasetsConverter.rst │ │ ├── bedhandler.rst │ │ ├── bigwighandler.rst │ │ ├── hdf5handler.rst │ │ ├── index.rst │ │ ├── tempnumpyarrayfiles.rst │ │ ├── textHandler.rst │ │ └── wighandler.rst │ ├── importer.rst │ ├── index.rst │ ├── normalizer.rst │ ├── statDist.rst │ ├── summary.rst │ └── util.rst ├── cmapNormalization.rst ├── commands │ ├── bc2cmap.rst │ ├── bed2h5.rst │ ├── bigWig2h5.rst │ ├── cmapImporter.rst │ ├── cmapNormalizer.rst │ ├── config.rst │ ├── coo2cmap.rst │ ├── encode2h5.rst │ ├── h5Converter.rst │ ├── hic2gcmap.rst │ ├── homer2cmap.rst │ ├── normIC.rst │ ├── normKR.rst │ ├── normMCFS.rst │ ├── normVC.rst │ ├── pairCoo2cmap.rst │ └── wig2h5.rst ├── conf.py ├── dLcmaps.rst ├── dlDatasetLinks.txt ├── downloadCCMapLinks.txt ├── faq.rst ├── file_formats.rst ├── images │ ├── axis.png │ ├── browser.png │ ├── browser_indexed.png │ ├── color-bar-dialog.png │ ├── colormap_dialog.png │ ├── dataset_selector.png │ ├── genome_track_options.png │ ├── h5Converter.png │ ├── importer.png │ ├── marker_options.png │ ├── normalizer.png │ ├── pageSize_dialog.png │ └── view-point.png ├── index.rst ├── install.rst ├── make.bat ├── mapBrowser.rst ├── modules_examples │ ├── access_ccmap_data.ipynb │ ├── access_gcmap_data.ipynb │ ├── compare_IC_norm.ipynb │ ├── compare_KR_norm.ipynb │ ├── export_ccmap.ipynb │ ├── import_ccmap.ipynb │ ├── index.rst │ ├── masked_array_ccmap.ipynb │ └── normalize_ccmap.ipynb ├── requirements.txt └── usage.rst ├── gcMapExplorer ├── __init__.py ├── _version.py ├── clui │ ├── __init__.py │ ├── bc2cmap.py │ ├── bed2h5.py │ ├── bigwig2h5.py │ ├── cmap2coo.py │ ├── config.py │ ├── coo2cmap.py │ ├── corrBWcmaps.py │ ├── encode2h5.py │ ├── hic2gcmap.py │ ├── homer2cmap.py │ ├── normIC.py │ ├── normKR.py │ ├── normMCFS.py │ ├── normVC.py │ ├── pairCoo2cmap.py │ └── wig2h5.py ├── config.py ├── gui │ ├── UIs │ │ ├── aboutBrowser.ui │ │ ├── correlationMaps.ui │ │ ├── dialogAxisProps.ui │ │ ├── dialogCustomPageSize.ui │ │ ├── gcmapSelectorForBrowser.ui │ │ ├── genomicDataSelector.ui │ │ ├── importer.ui │ │ ├── mainWindow.ui │ │ ├── mainWindow_old.ui │ │ ├── normalizer.ui │ │ ├── other1DFormatFileConversion.ui │ │ ├── textFileSelector.ui │ │ └── userColorMapDialog.ui │ ├── __init__.py │ ├── browser.py │ ├── browserHelpers.py │ ├── guiHelpers.py │ ├── h5Converter.py │ ├── icons │ │ ├── cmaps │ │ │ ├── afmhot.ico │ │ │ ├── afmhot_r.ico │ │ │ ├── autumn.ico │ │ │ ├── autumn_r.ico │ │ │ ├── blue_green.ico │ │ │ ├── blue_purple.ico │ │ │ ├── blues.ico │ │ │ ├── bone.ico │ │ │ ├── bone_r.ico │ │ │ ├── cool.ico │ │ │ ├── cool_r.ico │ │ │ ├── copper.ico │ │ │ ├── copper_r.ico │ │ │ ├── gist_heat.ico │ │ │ ├── gist_heat_r.ico │ │ │ ├── gray.ico │ │ │ ├── gray_r.ico │ │ │ ├── green_blue.ico │ │ │ ├── greens.ico │ │ │ ├── greys.ico │ │ │ ├── hot.ico │ │ │ ├── hot_r.ico │ │ │ ├── oranges.ico │ │ │ ├── oranges_red.ico │ │ │ ├── pink.ico │ │ │ ├── pink_r.ico │ │ │ ├── purple_blue.ico │ │ │ ├── purple_blue_green.ico │ │ │ ├── purple_red.ico │ │ │ ├── purples.ico │ │ │ ├── red_purples.ico │ │ │ ├── reds.ico │ │ │ ├── spring.ico │ │ │ ├── spring_r.ico │ │ │ ├── summer.ico │ │ │ ├── summer_r.ico │ │ │ ├── winter.ico │ │ │ ├── winter_r.ico │ │ │ ├── yellow_green.ico │ │ │ ├── yellow_green_blue.ico │ │ │ ├── yellow_orange_brown.ico │ │ │ └── yellow_orange_red.ico │ │ ├── downArrow.ico │ │ ├── downArrow.png │ │ ├── fitPlotsTight.png │ │ ├── gotoPlay.png │ │ ├── hspaceDecrement.png │ │ ├── hspaceIncrement.png │ │ ├── leftArrow.ico │ │ ├── leftArrow.png │ │ ├── leftDownArrow.ico │ │ ├── leftDownArrow.png │ │ ├── leftUpArrow.ico │ │ ├── leftUpArrow.png │ │ ├── resetArrow.ico │ │ ├── resetArrow.png │ │ ├── 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