Package: ExpressionCellNet 0.1.1

ExpressionCellNet: Network-Based Analysis of Gene Expression Perturbations

Network-centric framework for integrative analysis of high-throughput gene expression data using user-supplied gene-gene interaction graphs. Constructs seed-centered multi-generation networks constrained by expression correlations and simulates expression perturbation scenarios via regression-based prediction (van Dam, 2018).

Authors:Ehsan Keramati [aut, cre]

ExpressionCellNet_0.1.1.tar.gz
ExpressionCellNet_0.1.1.zip(r-4.7)ExpressionCellNet_0.1.1.zip(r-4.6)ExpressionCellNet_0.1.1.zip(r-4.5)
ExpressionCellNet_0.1.1.tgz(r-4.6-any)ExpressionCellNet_0.1.1.tgz(r-4.5-any)
ExpressionCellNet_0.1.1.tar.gz(r-4.7-any)ExpressionCellNet_0.1.1.tar.gz(r-4.6-any)
ExpressionCellNet_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ExpressionCellNet/json (API)

# Install 'ExpressionCellNet' in R:

install.packages('ExpressionCellNet', repos = c('https://ehsankeramatii.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

example_data - Example dataset for ExpressionCellNet

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 464 downloads 18 exports 35 dependencies

Last updated from:54e4ddcb70. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	136
source / vignettes	OK	183
linux-release-x86_64	OK	129
macos-release-arm64	OK	169
macos-oldrel-arm64	OK	191
windows-devel	OK	86
windows-release	OK	80
windows-oldrel	OK	109
wasm-release	OK	153

Exports:AnalyzeNetwork BuildNetwork CountMatrixNormalization createExpCellNetObj ExtractFeature FindPathway MeanExpression NetworkPrediction PCAforGenes PlotCorrelation PlotCountMatrix PlotNetworkPrediction PlotPathwayPrediction RegenerateTrainTest ShowHubGenes ShowNetwork ShowPathway UMAPforGenes

Dependencies:BH cli cpp11 crayon dqrng farver FNN ggplot2 glue gtable igraph irlba isoband labeling lattice lifecycle magrittr Matrix Metrics pkgconfig R6 RColorBrewer Rcpp RcppAnnoy RcppEigen RcppProgress rlang RSpectra S7 scales sitmo uwot vctrs viridisLite withr

Citation

Readme and manuals

Help Manual

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

Package: ExpressionCellNet 0.1.1

ExpressionCellNet: Network-Based Analysis of Gene Expression Perturbations

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)