# 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 1.13.0

- 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.