API for ubioinformat/TraRe
Transcriptional Rewiring
| Global functions | |
|---|---|
| .onAttach | Source code |
| LINKER_EvaluateTestSet | Man page Source code |
| LINKER_LearnRegulatoryPrograms | Man page Source code |
| LINKER_ReassignGenesToClusters | Man page Source code |
| LINKER_corrClust | Man page Source code |
| LINKER_extract_modules | Man page Source code |
| LINKER_init | Man page Source code |
| LINKER_run | Man page Source code |
| LINKER_runPhase1 | Man page Source code |
| LINKER_runPhase2 | Man page Source code |
| NET_compute_graph_all_LASSO1se | Man page Source code |
| NET_compute_graph_all_LASSOmin | Man page Source code |
| NET_compute_graph_all_LM | Man page Source code |
| NET_compute_graph_all_VBSR | Man page Source code |
| NET_run | Man page Source code |
| RemoveDuplicities | Source code |
| TraRe | Man page |
| TraRe-package | Man page |
| TraReClass | Man page |
| TraReClass-class | Man page |
| bipartiteGraphsSumm | Source code |
| compute_KL | Source code |
| correlationOfModuleGene | Source code |
| createLegendPlot | Source code |
| createModuleSummary | Man page Source code |
| create_html_summary | Man page Source code |
| create_index_page | Source code |
| cumSumTable | Source code |
| df_to_html | Source code |
| edgeinfo_from_graphs | Source code |
| expressionPlotsOfModuleGenes | Source code |
| expressionTableOfModuleGenes | Source code |
| extract_edge_strings_from_graph | Source code |
| extract_gene_row | Source code |
| fast_rew | Source code |
| filter_regulons | Source code |
| fishermeth | Source code |
| gen_heatmap | Man page Source code |
| geneOrder | Source code |
| generatecliques | Man page Source code |
| generategraph | Man page Source code |
| genetable_summary | Source code |
| getAvgVariance | Source code |
| getMaxVarName | Source code |
| getMaxVariance | Source code |
| getMedianCorrelation | Source code |
| getMedian_AvgVar | Source code |
| get_regulons | Source code |
| graph_to_modules | Source code |
| heatmapplot | Man page Source code |
| html_from_graph | Man page Source code |
| linker_create_index_page | Source code |
| linker_summarize_rungraphs | Source code |
| linker_write_html_table_page | Source code |
| linker_write_tables_all | Source code |
| maxrepeat | Source code |
| merge_regulons | Source code |
| module_edge_summary | Source code |
| module_node_summary | Source code |
| nullDistributionOfRewiringStatistic | Source code |
| orderGraphWeights | Man page Source code |
| plot_correlation_row | Man page Source code |
| plot_expression_row | Man page Source code |
| plot_gene_pair_scatter | Man page Source code |
| plot_gene_pair_scatter_by_class | Man page Source code |
| plot_igraph | Man page Source code |
| plotcliques | Man page Source code |
| preparedata | Man page Source code |
| preparerewiring | Man page Source code |
| rawsummary | Man page Source code |
| regulatorSummaryAndRank | Source code |
| return_layout | Man page Source code |
| return_layout_phenotype | Man page Source code |
| rewiring_add_phenotype | Man page Source code |
| rewiring_gene_level | Man page Source code |
| rewiring_regulon | Source code |
| rewiring_regulon_level | Man page Source code |
| rewiring_single_module | Source code |
| rewiring_test | Man page Source code |
| rewiring_test_pair_detail | Man page Source code |
| runrewiring | Man page Source code |
| selectmethod | Man page Source code |
| showfirstlast | Source code |
| summarize_module | Source code |
| superModuleStatistics | Source code |
| tab2cell | Source code |
| table2html | Source code |
| table2html_from_graph | Source code |
| trare_preprocessing | Man page Source code |
| vbsr | Source code |
| violinPlots | Source code |
| write_html_table_page | Source code |
| write_tables_all | Source code |
