addConnections_peak_gene | Add peak-gene connections to a 'GRN' object |
addConnections_TF_peak | Add TF-peak connections to a 'GRN' object |
addData | Add data to a 'GRN' object |
addData_TFActivity | Add TF activity data to GRN object using a simplified procedure for estimating it. EXPERIMENTAL. |
addTFBS | Add TFBS to a 'GRN' object |
add_TF_gene_correlation | Add TF-gene correlations to a 'GRN' object. The information is currently stored in 'GRN@connections$TF_genes.filtered'. Note that raw p-values are not adjusted. |
AR_classification_wrapper | Run the activator-repressor classification for the TFs for a 'GRN' object |
build_eGRN_graph | Builds a graph out of a set of connections |
calculateCommunitiesEnrichment | Enrichment analysis for the genes in each community in the filtered 'GRN' |
calculateCommunitiesStats | Generate graph communities and their summarizing statistics |
calculateGeneralEnrichment | Run an enrichment analysis for the genes in the filtered 'GRN' |
calculateTFEnrichment | Calculate TF-based GO enrichment |
changeOutputDirectory | Change the output directory of a GRN object |
deleteIntermediateData | Optional convenience function to delete intermediate data from the function 'AR_classification_wrapper' and summary statistics that may occupy a lot of space |
filterData | Filter data from a 'GRN' object |
filterGRNAndConnectGenes | Filter the GRN and integrate peak-gene connections. |
generateStatsSummary | Generate a summary PDF for the number of connections for a 'GRN' object. |
genes | Get the number of genes for a 'GRN' object. |
getCounts | Get counts for the various data defined in a 'GRN' object |
getGRNConnections | Extract connections from a 'GRN' object |
getParameters | Retrieve parameters for previously used function calls and general parameters for a 'GRN' object. |
getTopNodes | Retrieve top Nodes in the filtered 'GRN' |
GRaNIE | *GRaNIE* (*G*ene *R*egul*a*tory *N*etwork *I*nference including *E*nhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information) |
GRN-class | Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (*eGRNs*) |
importTFData | Import externally derived TF Activity data. EXPERIMENTAL. |
initializeGRN | Initialize a 'GRN' object |
loadExampleObject | Load example GRN dataset |
nGenes | Get the number of genes for a 'GRN' object. |
nPeaks | Get the number of peaks for a 'GRN' object. |
overlapPeaksAndTFBS | Overlap peaks and TFBS for a 'GRN' object |
peaks | Get the number of peaks for a 'GRN' object. |
performAllNetworkAnalyses | Perform all network-related statistical and descriptive analyses, including community and enrichment analyses. |
plotCommunitiesEnrichment | Plot community-based enrichment results |
plotCommunitiesStats | Plot general structure & connectivity statistics for each community in a filtered 'GRN' |
plotDiagnosticPlots_peakGene | Plot diagnostic plots for peak-gene connections for a 'GRN' object |
plotDiagnosticPlots_TFPeaks | Plot diagnostic plots for TF-peak connections for a 'GRN' object |
plotGeneralEnrichment | Plot the general enrichement results |
plotGeneralGraphStats | Plot general structure and connectivity statistics for a filtered 'GRN' |
plotPCA_all | Produce a PCA plot of the data from a 'GRN' object |
plotTFEnrichment | Plot TF-based GO enrichment results |
plot_stats_connectionSummary | Plot various network connectivity summaries for a 'GRN' object |
visualizeGRN | Visualize a filtered GRN. |