Package: DNEA 1.3.0

Christopher Patsalis

DNEA: Differential Network Enrichment Analysis for Biological Data

The DNEA R package is the latest implementation of the Differential Network Enrichment Analysis algorithm and is the successor to the Filigree Java-application described in Iyer et al. (2020). The package is designed to take as input an m x n expression matrix for some -omics modality (ie. metabolomics, lipidomics, proteomics, etc.) and jointly estimate the biological network associations of each condition using the DNEA algorithm described in Ma et al. (2019). This approach provides a framework for data-driven enrichment analysis across two experimental conditions that utilizes the underlying correlation structure of the data to determine feature-feature interactions.

Authors:Christopher Patsalis [cre, aut], Gayatri Iyer [aut], Alla Karnovsky [fnd], George Michailidis [fnd]

DNEA_1.3.0.tar.gz
DNEA_1.3.0.zip(r-4.7)DNEA_1.3.0.zip(r-4.6)DNEA_1.3.0.zip(r-4.5)
DNEA_1.3.0.tgz(r-4.6-any)DNEA_1.3.0.tgz(r-4.5-any)
DNEA_1.3.0.tar.gz(r-4.7-any)DNEA_1.3.0.tar.gz(r-4.6-any)
DNEA_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DNEA/json (API)

# Install 'DNEA' in R:

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

Bug tracker:https://github.com/karnovsky-lab/dnea/issues

Datasets:

dnw - Example results for DNEA
metab_data - Feature meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial
T1Dmeta - Sample meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial
TEDDY - Example expresion data set from The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial

On BioConductor:DNEA-1.3.0(bioc 3.24)DNEA-1.2.0(bioc 3.23)

metabolomics proteomics lipidomics differentialexpression networkenrichment network clustering dataimport bioinformatics network-analysis rstudio

4.78 score 3 stars 2 scripts 185 downloads 41 exports 119 dependencies

Last updated from:3efd42f7ca. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	216
linux-devel-x86_64	NOTE	625
source / vignettes	OK	372
linux-release-x86_64	NOTE	682
macos-release-arm64	NOTE	339
macos-oldrel-arm64	NOTE	358
windows-devel	NOTE	956
windows-release	NOTE	558
windows-oldrel	NOTE	981
wasm-release	OK	232

Exports:addExpressionData adjacencyGraph adjacencyMatrix aggregateFeatures BICscores BICscores<-BICtune CCsummary clusterNet createDNEAobject datasetSummary diagnostics edgeList expressionData featureNames filterNetworks getNetworkFiles getNetworks includeMetadata lambdas2Test massDataset2DNEA metaData netGSAresults networkGroupIDs networkGroupIDs<-networkGroups nodeList numFeatures numSamples optimizedLambda optimizedLambda<-plotNetworks projectName runNetGSA sampleNames selectionProbabilities selectionResults show stabilitySelection subnetworkMembership sumExp2DNEA

Dependencies:abind annotate AnnotationDbi askpass assertthat babelgene backports base64enc base64url BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem caTools cli codetools corpcor cpp11 crayon curl data.table DBI DelayedArray digest dir.expiry dplyr evaluate fastmap filelock foreach formatR fs futile.logger futile.options gdata genefilter generics GenomicRanges glasso glassoFast glmnet glue gplots graph graphite gtools hms htmltools httr igraph IRanges IRdisplay IRkernel iterators janitor jsonlite KEGGREST KernSmooth lambda.r lattice lifecycle lubridate magrittr Matrix MatrixGenerics matrixStats memoise mime msigdbr netgsa openssl pbdZMQ pillar pkgconfig plyr png purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl RCy3 repr reshape2 RJSONIO rlang RSQLite S4Arrays S4Vectors Seqinfo shape snakecase snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange utf8 uuid vctrs withr XML xtable XVector

Differential Network Expression Analysis for Metabolomics Data

Rendered fromDNEA.Rmdusingknitr::rmarkdown

Last update: 2025-04-23
Started: 2023-08-23

Help page	Topics
DNEA: Differential Network Enrichment Analysis for Biological Data	DNEA-package DNEA
Include custom normalized data in the DNEA object	addExpressionData
Retrieve the adjacency graph for the case, control, or joint network	adjacencyGraph adjacencyGraph,consensusClusteringResults-method adjacencyGraph,DNEA-method
Retrieve the weighted or unweighted adjacency matrix	adjacencyMatrix adjacencyMatrix,DNEA-method
Aggregate correlated features into a single feature class	aggregateFeatures
Access the BIC scores for each lambda value evaluated	BICscores BICscores,DNEA-method BICscores<- BICscores<-,DNEA-method
Optimize the lambda regularization parameter for the glasso-based network models using Bayesian-information Criterion	BICtune BICtune,DNEA-method BICtune,matrix-method
Retrieves the summary results of consensus clustering	CCsummary CCsummary,DNEA-method
Identify metabolic modules within the biological networks using a consensus clustering approach	clusterNet
collapsed_DNEA	collapsed_DNEA collapsed_DNEA-class
consensusClusteringResults	consensusClusteringResults consensusClusteringResults-class
Initialize a DNEA object	createDNEAobject
Access the dataset_summary slot of a DNEA object	datasetSummary datasetSummary,DNEA-method
Retrieve the diagnostic values for the input expression data	diagnostics diagnostics,DNEA-method diagnostics,DNEAinputSummary-method
DNEA object	DNEA-class show,DNEA-method
DNEAinputSummary	DNEAinputSummary DNEAinputSummary-class show,DNEAinputSummary-method
Example results for DNEA	dnw
Access the edge list	edgeList edgeList,DNEA-method edgeList<- edgeList<-,DNEA-method
Access expression data within a DNEA object,	expressionData expressionData,DNEA-method
Retrieve the feature names from the metadata slot.	featureNames featureNames,DNEA-method
Filter the adjacency matrices to only the edges that meet the filter conditions	filterNetworks filterNetworks,DNEA-method filterNetworks,list-method
Save network information to .csv files	getNetworkFiles
Construct the GLASSO-based biological Networks	getNetworks
Add additional metadata to the DNEA object	includeMetadata
Access the lambda values tested during hyper parameter optimization	lambdas2Test lambdas2Test,DNEA-method
Initialize a DNEA object from a mass_dataset object	massDataset2DNEA
Feature meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial	metab_data
Retrieve metadata stored in a DNEA	metaData metaData,DNEA-method
Access the netGSA slot of a DNEA object	netGSAresults netGSAresults,DNEA-method
Access and set the experimental group labels	networkGroupIDs networkGroupIDs,DNEA-method networkGroupIDs<-
Retrieve the unique group values of the experimental condition	networkGroups networkGroups,DNEA-method
Access the node list	nodeList nodeList,DNEA-method nodeList<- nodeList<-,DNEA-method
Retrieve the total number of features in the dataset	numFeatures numFeatures,DNEA-method numFeatures,DNEAinputSummary-method
Retrieves the total number of samples in the dataset	numSamples numSamples,DNEA-method numSamples,DNEAinputSummary-method
Access the lambda value used in analysis	optimizedLambda optimizedLambda,DNEA-method optimizedLambda<- optimizedLambda<-,DNEA-method
Visualize the biological networks	plotNetworks
Return the name of the current experiment	projectName projectName,DNEA-method
Identify metabolic modules that are enriched across experimental conditions using NetGSA	runNetGSA
Retrieve the sample names from the metadata slot.	sampleNames sampleNames,DNEA-method
Access and set the edge selection probabilities from stabilitySelection()	selectionProbabilities selectionProbabilities,DNEA-method
Access and set the edge selection results from stabilitySelection()	selectionResults selectionResults,DNEA-method
Stability selection calculates selection probabilities for every possible feature-feature interaction within the input data	stabilitySelection
Retrieve the subnetwork membership for each feature	subnetworkMembership subnetworkMembership,consensusClusteringResults-method subnetworkMembership,DNEA-method
Initialize a DNEA from SummarizedExperiment	sumExp2DNEA
Sample meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial	T1Dmeta
Example expresion data set from The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial	TEDDY

Package: DNEA 1.3.0

DNEA: Differential Network Enrichment Analysis for Biological Data

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