API for chrarnold/GRaNIE
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
| Global functions | |
|---|---|
| .addFunctionLogToObject | Source code |
| .addStats | Source code |
| .asMatrixFromSparse | Source code |
| .asSparseMatrix | Source code |
| .buildGraph | Source code |
| .calcGCContentPeaks | Source code |
| .calculatePeakGeneCorrelations | Source code |
| .calculatePeakGeneOverlaps | Source code |
| .calculate_classificationThresholds | Source code |
| .checkAndLoadPackages | Source code |
| .checkAndLoadPackagesGenomeAssembly | Source code |
| .checkAndLogWarningsAndErrors | Source code |
| .checkAndUpdateConnectionTypes | Source code |
| .checkEnrichmentCongruence_general_community | Source code |
| .checkForbiddenNames | Source code |
| .checkOntologyPackageInstallation | Source code |
| .checkSelfOverlap | Source code |
| .classFreq_label | Source code |
| .clearOpenDevices | Source code |
| .combineEnrichmentResults | Source code |
| .computeForegroundAndBackgroundMatrices | Source code |
| .computeTF_peak.fdr | Source code |
| .constructGRanges | Source code |
| .correlateData | Source code |
| .correlateMatrices | Source code |
| .createConsensusPeaksDF | Source code |
| .createFileList | Source code |
| .createGRNObject | Source code |
| .createTables_peakGeneQC | Source code |
| .customLabeler | Source code |
| .drawCombinedHeatmap | Source code |
| .execInParallelGen | Source code |
| .filterPeaksByChromosomeAndSize | Source code |
| .filterPeaksByRowMeans | Source code |
| .filterSortAndShuffle_peakTF_overlapTable | Source code |
| .finalizeClassificationAndAppend | Source code |
| .findSuitableColumnsToPlot | Source code |
| .generateTF_GC_diagnosticPlots | Source code |
| .getAllGeneTypesAndFrequencies | Source code |
| .getBackgroundGenes | Source code Source code |
| .getChrLengths | Source code |
| .getDegreeStats | Source code |
| .getFinalListOfTFs | Source code |
| .getGenomeObject | Source code |
| .getKnownGeneAnnotationNew | Source code |
| .getPermutationSuffixStr | Source code |
| .initBiocParallel | Source code |
| .initializeStatsDF | Source code |
| .intersectData | Source code |
| .intersectTFBSPeaks | Source code |
| .my.mean | Source code |
| .my.median | Source code |
| .normalizeCounts | Source code |
| .normalizeNewDataWrapper | Source code |
| .onAttach | Source code |
| .optimizeSpaceGRN | Source code |
| .performIHW | Source code |
| .plotDensity | Source code |
| .plotDiagnosticPlots_peakGene_all | Source code |
| .plotEnrichmentGeneral | Source code |
| .plotPCA_QC | Source code |
| .plotTF_peak_GC_diagnosticPlots | Source code |
| .plotTF_peak_TFActivity_QC | Source code |
| .plot_AR_thresholds | Source code |
| .plot_PCA_wrapper | Source code |
| .plot_TF_peak_fdr | Source code |
| .plot_classCorrelations | Source code |
| .plot_density | Source code |
| .plot_heatmapAR | Source code |
| .plot_stats_connectionSummaryBoxplot | Source code |
| .plot_stats_connectionSummaryDensity | Source code |
| .plot_stats_connectionSummaryHeatmap | Source code |
| .populateGOAnnotation | Source code |
| .prettyNum | Source code |
| .printExecutionTime | Source code |
| .printGraphSummary | Source code |
| .printLoopsGraph | Source code |
| .printMultipleEdges | Source code |
| .printMultipleGraphsPerPage | Source code |
| .printParametersLog | Source code |
| .printWarningPageNumber | Source code |
| .readHOCOMOCOTable | Source code |
| .readTFBSFile | Source code |
| .read_tidyverse_wrapper | Source code |
| .removeScientificNotation_positions | Source code |
| .retrieveAnnotationData | Source code |
| .runEnrichment | Source code |
| .selectCommunitesByRank | Source code |
| .shuffleColumns | Source code |
| .shuffleRowsPerColumn | Source code |
| .startLogger | Source code |
| .testExistanceAndCreateDirectoriesRecursively | Source code |
| .validGRNObj | Source code |
| AR_classification_wrapper | Man page |
| GRN-class | Man page |
| GRaNIE | Man page |
| addConnections_TF_peak | Man page |
| addConnections_peak_gene | Man page Source code |
| addData | Man page Source code |
| addData_TFActivity | Man page Source code |
| addSNPOverlap | Source code |
| addTFBS | Man page Source code |
| add_TF_gene_correlation | Man page Source code |
| build_eGRN_graph | Man page Source code |
| calculateCommunitiesEnrichment | Man page Source code |
| calculateCommunitiesStats | Man page Source code |
| calculateGeneralEnrichment | Man page Source code |
| calculateTFEnrichment | Man page Source code |
| changeOutputDirectory | Man page Source code |
| deleteIntermediateData | Man page Source code |
| filterData | Man page |
| filterGRNAndConnectGenes | Man page Source code |
| generateStatsSummary | Man page Source code |
| genes | Man page |
| getBasic_metadata_visualization | Source code |
| getCounts | Man page Source code |
| getGRNConnections | Man page Source code |
| getParameters | Man page |
| getTopNodes | Man page Source code |
| importTFData | Man page Source code |
| initializeGRN | Man page Source code |
| isIntegerMatrix | Source code |
| loadExampleObject | Man page Source code |
| nGenes | Man page Source code |
| nPeaks | Man page Source code |
| overlapPeaksAndTFBS | Man page Source code |
| peaks | Man page |
| performAllNetworkAnalyses | Man page Source code |
| plotCommunitiesEnrichment | Man page Source code |
| plotCommunitiesStats | Man page Source code |
| plotDiagnosticPlots_TFPeaks | Man page Source code |
| plotDiagnosticPlots_peakGene | Man page Source code |
| plotGeneralEnrichment | Man page Source code |
| plotGeneralGraphStats | Man page Source code |
| plotPCA_all | Man page Source code |
| plotTFEnrichment | Man page Source code |
| plot_stats_connectionSummary | Man page Source code |
| visualizeGRN | Man page |
