Index A | C | D | E | F | G | H | I | J | L | M | O | P | Q | R | S | T | U | W A addRandom() (in module PopPUNK.sketchlib) api() (in module PopPUNK.web) assign_query() (in module PopPUNK.assign) assign_query_hdf5() (in module PopPUNK.assign) C calc_prevalence() (in module PopPUNK.web) check_and_set_gpu() (in module PopPUNK.utils) checkSketchlibLibrary() (in module PopPUNK.sketchlib) checkSketchlibVersion() (in module PopPUNK.sketchlib) constructDatabase() (in module PopPUNK.sketchlib) createDatabaseDir() (in module PopPUNK.sketchlib) createMicroreact() (in module PopPUNK.plot) D decisionBoundary() (in module PopPUNK.utils) distHistogram() (in module PopPUNK.plot) drawMST() (in module PopPUNK.plot) E evaluate_dbscan_clusters() (in module PopPUNK.dbscan) F findBetweenLabel() (in module PopPUNK.dbscan) findBetweenLabel_bgmm() (in module PopPUNK.bgmm) findWithinLabel() (in module PopPUNK.bgmm) fit2dMultiGaussian() (in module PopPUNK.bgmm) fitDbScan() (in module PopPUNK.dbscan) fitKmerCurve() (in module PopPUNK.sketchlib) G generate_embedding() (in module PopPUNK.mandrake) get_database_statistics() (in module PopPUNK.sketchlib) get_grid() (in module PopPUNK.plot) get_match_search_depth() (in module PopPUNK.utils) getKmersFromReferenceDatabase() (in module PopPUNK.sketchlib) getSeqsInDb() (in module PopPUNK.sketchlib) getSketchSize() (in module PopPUNK.sketchlib) graphml_to_json() (in module PopPUNK.web) H highlight_cluster() (in module PopPUNK.web) I isolateNameToLabel() (in module PopPUNK.utils) iterDistRows() (in module PopPUNK.utils) J joinClusterDicts() (in module PopPUNK.utils) joinDBs() (in module PopPUNK.sketchlib) L listDistInts() (in module PopPUNK.utils) log_likelihood() (in module PopPUNK.bgmm) log_multivariate_normal_density() (in module PopPUNK.bgmm) M main() (in module PopPUNK.assign) (in module PopPUNK.visualise) module PopPUNK.assign PopPUNK.bgmm PopPUNK.dbscan PopPUNK.mandrake PopPUNK.plot PopPUNK.sketchlib PopPUNK.utils PopPUNK.visualise PopPUNK.web O outputsForCytoscape() (in module PopPUNK.plot) outputsForGrapetree() (in module PopPUNK.plot) outputsForMicroreact() (in module PopPUNK.plot) outputsForPhandango() (in module PopPUNK.plot) P plot_contours() (in module PopPUNK.plot) plot_database_evaluations() (in module PopPUNK.plot) plot_dbscan_results() (in module PopPUNK.plot) plot_evaluation_histogram() (in module PopPUNK.plot) plot_fit() (in module PopPUNK.plot) plot_refined_results() (in module PopPUNK.plot) plot_results() (in module PopPUNK.plot) plot_scatter() (in module PopPUNK.plot) PopPUNK.assign module PopPUNK.bgmm module PopPUNK.dbscan module PopPUNK.mandrake module PopPUNK.plot module PopPUNK.sketchlib module PopPUNK.utils module PopPUNK.visualise module PopPUNK.web module Q queryDatabase() (in module PopPUNK.sketchlib) R read_rlist_from_distance_pickle() (in module PopPUNK.utils) readDBParams() (in module PopPUNK.sketchlib) readIsolateTypeFromCsv() (in module PopPUNK.utils) readPickle() (in module PopPUNK.utils) readRfile() (in module PopPUNK.utils) removeFromDB() (in module PopPUNK.sketchlib) S set_env() (in module PopPUNK.utils) setupDBFuncs() (in module PopPUNK.utils) sketch_to_hdf5() (in module PopPUNK.web) stderr_redirected() (in module PopPUNK.utils) storePickle() (in module PopPUNK.utils) summarise_clusters() (in module PopPUNK.web) T transformLine() (in module PopPUNK.utils) U update_distance_matrices() (in module PopPUNK.utils) update_maps_timelines() (in module PopPUNK.plot) W writeClusterCsv() (in module PopPUNK.plot)