Package index • NOVA

Core Analysis

Main functions for cell-cell communication inference

ExtractEdges(): Extract Ligand-Receptor Mediated Interactions
FilterEdges(): Filter Edges
GetEdges(): Get Edges for Specific Cluster Pairs
extract_edges: Extract Ligand-Receptor Mediated Cell-Cell Communication

Differential Analysis

Compare communication between conditions

DiffEdges(): Compare Cell-Cell Communication Between Conditions
SummarizeByCluster(): Summarize Differential Results by Cluster Pair
SummarizeByLR(): Summarize Differential Results by LR Pair
ExportDiff(): Export Differential Results
diff_edges: Differential Cell-Cell Communication Analysis

Visualization

Plotting functions for communication networks

PlotHeatmap(): Plot Communication Heatmap
PlotNetwork(): Plot Communication Network
PlotChord(): Plot Chord Diagram
PlotLRPairs(): Plot LR Pairs Between Clusters
PlotDiffHeatmap(): Plot Differential Heatmap
PlotVolcano(): Plot Volcano
SavePlot(): Save Plot
nova_palette(): NOVA Color Palette
visualization: NOVA Visualization Functions

Data & Database

Ligand-receptor database and homology mapping

GetLRDatabase(): Get Ligand-Receptor Database
GetHomologyMapping(): Get Homology Mapping
ConvertGeneSymbols(): Convert Gene Symbols Between Species
ConvertIDsToSymbols(): Convert Gene IDs to Symbols
supported_species(): Supported species mapping
supported_id_types(): Supported gene ID types
data: NOVA Data Access Functions

Seurat Integration

Functions for Seurat object compatibility

SeuratToNOVA(): Convert Seurat Object to NOVA Input
GetExpressionMatrix(): Get Expression Matrix from Seurat Object
GetCellMetadata(): Get Cell Metadata from Seurat Object
GetClusters(): Get Cluster Identities from Seurat Object
AddNOVAResults(): Add NOVA Results to Seurat Object
seurat_compat: Seurat Compatibility Layer

Result Objects

S3 methods for result objects

print(<NOVAResult>): Print NOVAResult
summary(<NOVAResult>): Summary of NOVAResult
print(<NOVADiffResult>): Print NOVADiffResult
summary(<NOVADiffResult>): Summary of NOVADiffResult

Package Info

Package documentation

NOVA NOVA-package: NOVA: Network Of Versatile Cell-Cell Communication Analysis