## All functions

AR_classification_wrapper()

Run the activator-repressor classification for the TFs for a GRN object

GRN-class

Create, represent, investigate, quantify and visualize enhancer-mediated gene regulatory networks (eGRNs)

GRaNIE

GRaNIE (Gene Regulatory Network Inference including Enhancers): Reconstruction and evaluation of data-driven, cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNAseq data (general package information)

addConnections_TF_peak()

Add TF-peak connections to a GRN object

addConnections_peak_gene()

Add peak-gene 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.

add_featureVariation()

Quantify and interpret multiple sources of biological and technical variation for features (TFs, peaks, and genes) in a GRN object

build_eGRN_graph()

Builds a graph out of a set of connections

calculateCommunitiesEnrichment()

Run an enrichment analysis for the genes in each community in the filtered GRN object

calculateCommunitiesStats()

Generate graph communities and their summarizing statistics

calculateGeneralEnrichment()

Run an enrichment analysis for the genes in the whole network in the filtered GRN object

calculateTFEnrichment()

Run an enrichment analysis for the set of genes connected to a particular TF or sets of TFs in the filtered GRN object

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 RNA-seq and/or peak data from a GRN object

filterGRNAndConnectGenes()

Filter TF-peaks and peak-gene connections and combine them to TF-peak-gene connections to construct an eGRN.

generateStatsSummary()

Generate a summary for the number of connections for different filtering criteria for a GRN object.

getCounts()

Get counts for the various data defined in a GRN object

getGRNConnections()

Extract connections or links from a GRN object as a data frame.

getParameters()

Retrieve parameters for previously used function calls and general parameters for a GRN object.

getTopNodes()

Retrieve the top nodes (TFs or genes) with respect to either degree or Eigenvector centrality in the filtered GRN object.

importTFData()

Import externally derived TF Activity data. EXPERIMENTAL.

initializeGRN()

Create and initialize an empty GRN object.

loadExampleObject()

nGenes()

Get the number of genes for a GRN object.

nPeaks()

Get the number of peaks for a GRN object.

nTFs()

Get the number of TFs for a GRN object.

overlapPeaksAndTFBS()

Overlap peaks and TFBS for a GRN object

performAllNetworkAnalyses()

Perform all network-related statistical and descriptive analyses, including community and enrichment analyses. See the functions it executes in the @seealso section below.

plotCommunitiesEnrichment()

Plot community-based enrichment results for a filtered GRN object

plotCommunitiesStats()

Plot general structure & connectivity statistics for each community in a filtered GRN

plotDiagnosticPlots_TFPeaks()

Plot diagnostic plots for TF-peak connections for a GRN object

plotDiagnosticPlots_TFPeaks_GC()

Plot GC-specific diagnostic plots for TF-peak connections for a GRN object

plotDiagnosticPlots_peakGene()

Plot diagnostic plots for peak-gene connections for a GRN object

plotGeneralEnrichment()

Plot the general enrichement results

plotGeneralGraphStats()

Plot general structure and connectivity statistics for a filtered GRN object

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 eGRN in a flexible manner.