Man pages for chrarnold/GRaNIE
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
| 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... |
| addTFBS | Add TFBS to a 'GRN' object |
| add_TF_gene_correlation | Add TF-gene correlations to a 'GRN' object. The information... |
| AR_classification_wrapper | Run the activator-repressor classification for the TFs for a... |
| build_eGRN_graph | Builds a graph out of a set of connections |
| calculateCommunitiesEnrichment | Enrichment analysis for the genes in each community in the... |
| calculateCommunitiesStats | Generate graph communities and their summarizing statistics |
| calculateGeneralEnrichment | Run an enrichment analysis for the genes in the filtered... |
| calculateTFEnrichment | Calculate TF-based GO enrichment |
| changeOutputDirectory | Change the output directory of a GRN object |
| deleteIntermediateData | Optional convenience function to delete intermediate data... |
| 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... |
| genes-methods | 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... |
| getTopNodes | Retrieve top Nodes in the filtered 'GRN' |
| GRaNIE | *GRaNIE* (*G*ene *R*egul*a*tory *N*etwork *I*nference... |
| GRN-class | Create, represent, investigate, quantify and visualize... |
| importTFData | Import externally derived TF Activity data. EXPERIMENTAL. |
| initializeGRN | Initialize a 'GRN' object |
| loadExampleObject | Load example GRN dataset |
| overlapPeaksAndTFBS | Overlap peaks and TFBS for a 'GRN' object |
| peaks-methods | Get the number of peaks for a 'GRN' object. |
| performAllNetworkAnalyses | Perform all network-related statistical and descriptive... |
| plotCommunitiesEnrichment | Plot community-based enrichment results |
| plotCommunitiesStats | Plot general structure & connectivity statistics for each... |
| plotDiagnosticPlots_peakGene | Plot diagnostic plots for peak-gene connections for a 'GRN'... |
| plotDiagnosticPlots_TFPeaks | Plot diagnostic plots for TF-peak connections for a 'GRN'... |
| plotGeneralEnrichment | Plot the general enrichement results |
| plotGeneralGraphStats | Plot general structure and connectivity statistics for a... |
| plotPCA_all | Produce a PCA plot of the data from a 'GRN' object |
| plot_stats_connectionSummary | Plot various network connectivity summaries for a 'GRN'... |
| plotTFEnrichment | Plot TF-based GO enrichment results |
| visualizeGRN | Visualize a filtered GRN. |
