Network-Based Analysis of Gene Expression Perturbations

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Documentation for package ‘ExpressionCellNet’ version 0.1.1

• DESCRIPTION file

Help Pages

AnalyzeNetwork	Analyze network topology and identify hub genes
BuildNetwork	Construct a gene interaction network centered on a seed gene
CountMatrixNormalization	Normalize expression count matrix
createExpCellNetObj	Create an ExpressionCellNet object
example_data	Example dataset for ExpressionCellNet
ExtractFeature	Extract network-derived expression features
FindPathway	Find the shortest path between two genes in the network
MeanExpression	Compute mean expression of a gene
NetworkPrediction	Predict network-wide expression changes after perturbing a seed gene
PCAforGenes	PCA on network-derived features
PlotCorrelation	Plot correlation between two genes
PlotCountMatrix	Plot expression matrix distribution
PlotNetworkPrediction	Plot network prediction summary
PlotPathwayPrediction	Plot pathway-restricted prediction to a target gene
RegenerateTrainTest	Regenerate train/test split
ShowHubGenes	Show hub genes on the network
ShowNetwork	Visualize the constructed network
ShowPathway	Visualize a pathway (highlighted subgraph)
UMAPforGenes	UMAP on network-derived features