GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using single-cell or bulk chromatin accessibility and RNA-seq data

---

Documentation for package ‘GRaNIE’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

GRaNIE-package	*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)
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.
addSNPData	Add SNP data to a 'GRN' object and associate SNPs to peaks.
addTFBS	Add TFBS 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
add_TF_gene_correlation	Add TF-gene correlations to a 'GRN' object.
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	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
filterConnectionsForPlotting	Filter connections for subsequent visualization with 'visualizeGRN()' from the filtered eGRN
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.
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 or links from a 'GRN' object as a data frame.
getGRNSummary	Summarize a 'GRN' object to a named list for comparison with other 'GRN' objects.
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.
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	Create and initialize an empty '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.
nTFs	Get the number of TFs 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. 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'
plotCorrelations	Plot scatter plots of the underlying count data for either TF-peak, peak-gene or TF-gene pairs for a 'GRN' object
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
plotDiagnosticPlots_TFPeaks_GC	Plot GC-specific 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' 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
TFs	Get the number of TFs for a 'GRN' object.
visualizeGRN	Visualize a filtered eGRN in a flexible manner.