% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Help.R
\docType{package}
\name{ExpressionCellNet}
\alias{ExpressionCellNet}
\title{ExpressionCellNet: Network-centric modeling of gene expression perturbations}
\description{
ExpressionCellNet provides an integrative workflow for constructing biologically
constrained gene–gene interaction networks by combining curated interaction evidence
with statistically supported expression correlations. Built networks can be analyzed
using centrality metrics, hub-gene identification, shortest-path queries, and
enrichment analysis. The framework also supports regression-based prediction to
simulate in silico perturbations (e.g., gene silencing/overexpression) and to
estimate how expression changes propagate through connected genes.
}
\section{Core workflow}{

\enumerate{
  \item Create object: \code{createExpCellNetObj()}
  \item Normalize/filter: \code{CountMatrixNormalization()}
  \item Build network: \code{BuildNetwork()}
  \item Network analysis: \code{AnalyzeNetwork()}, \code{ShowHubGenes()}, \code{FindPathway()}
  \item Prediction and visualization: \code{NetworkPrediction()}, \code{PlotNetworkPrediction()}
  \item Dimension reduction: \code{PCAforGenes()}, \code{UMAPforGenes()}
}
}

\section{Main functions}{

\describe{
  \item{\code{createExpCellNetObj}}{Create the main analysis object.}
  \item{\code{CountMatrixNormalization}}{Filter and normalize count matrices (CPM/log2).}
  \item{\code{BuildNetwork}}{Construct a multi-generation network from a seed gene.}
  \item{\code{AnalyzeNetwork}}{Compute centrality metrics and extract hub genes (top 10\%).}
  \item{\code{FindPathway}}{Shortest path between two genes in the constructed network.}
  \item{\code{NetworkPrediction}}{Predict expression response to gene perturbation.}
}
}

\section{Input data}{

Required inputs typically include:
\itemize{
  \item A gene-by-sample expression matrix (counts or expression values)
  \item A gene annotation table with consistent gene identifiers
  \item A curated gene gene interaction database (two-column edge list)
}
}

\section{Notes}{

This package is intended for decision support and hypothesis generation and does not
claim causal inference.
}

\seealso{
Useful links:
\itemize{
  \item \doi{10.1093/bib/bbw139}
}

}
\author{
\strong{Maintainer}: Ehsan Keramati \email{ehsan.keramati14@gmail.com}

}
\keyword{internal}
