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✨
card.svg |card.png
DNEA/json (API)
NEWS

# 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)

metabolomicsproteomicslipidomicsdifferentialexpressionnetworkenrichmentnetworkclusteringdataimportbioinformaticsnetwork-analysisrstudio

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

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

TargetResultTimeFilesSyslog
bioc-checksNOTE216
linux-devel-x86_64NOTE625
source / vignettesOK372
linux-release-x86_64NOTE682
macos-release-arm64NOTE339
macos-oldrel-arm64NOTE358
windows-develNOTE956
windows-releaseNOTE558
windows-oldrelNOTE981
wasm-releaseOK232

Exports:addExpressionDataadjacencyGraphadjacencyMatrixaggregateFeaturesBICscoresBICscores<-BICtuneCCsummaryclusterNetcreateDNEAobjectdatasetSummarydiagnosticsedgeListexpressionDatafeatureNamesfilterNetworksgetNetworkFilesgetNetworksincludeMetadatalambdas2TestmassDataset2DNEAmetaDatanetGSAresultsnetworkGroupIDsnetworkGroupIDs<-networkGroupsnodeListnumFeaturesnumSamplesoptimizedLambdaoptimizedLambda<-plotNetworksprojectNamerunNetGSAsampleNamesselectionProbabilitiesselectionResultsshowstabilitySelectionsubnetworkMembershipsumExp2DNEA

Dependencies:abindannotateAnnotationDbiaskpassassertthatbabelgenebackportsbase64encbase64urlBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemcaToolsclicodetoolscorpcorcpp11crayoncurldata.tableDBIDelayedArraydigestdir.expirydplyrevaluatefastmapfilelockforeachformatRfsfutile.loggerfutile.optionsgdatagenefiltergenericsGenomicRangesglassoglassoFastglmnetgluegplotsgraphgraphitegtoolshmshtmltoolshttrigraphIRangesIRdisplayIRkerneliteratorsjanitorjsonliteKEGGRESTKernSmoothlambda.rlatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimemsigdbrnetgsaopensslpbdZMQpillarpkgconfigplyrpngpurrrquadprogR6rappdirsRColorBrewerRcppRcppEigenRCurlRCy3reprreshape2RJSONIOrlangRSQLiteS4ArraysS4VectorsSeqinfoshapesnakecasesnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangeutf8uuidvctrswithrXMLxtableXVector

Differential Network Expression Analysis for Metabolomics Data

Christopher P. Patsalis

Rendered fromDNEA.Rmdusingknitr::rmarkdownon May 30 2026.

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

Readme and manuals

Help Manual

Help pageTopics
DNEA: Differential Network Enrichment Analysis for Biological DataDNEA-package DNEA
Include custom normalized data in the DNEA objectaddExpressionData
Retrieve the adjacency graph for the case, control, or joint networkadjacencyGraph adjacencyGraph,consensusClusteringResults-method adjacencyGraph,DNEA-method
Retrieve the weighted or unweighted adjacency matrixadjacencyMatrix adjacencyMatrix,DNEA-method
Aggregate correlated features into a single feature classaggregateFeatures
Access the BIC scores for each lambda value evaluatedBICscores BICscores,DNEA-method BICscores<- BICscores<-,DNEA-method
Optimize the lambda regularization parameter for the glasso-based network models using Bayesian-information CriterionBICtune BICtune,DNEA-method BICtune,matrix-method
Retrieves the summary results of consensus clusteringCCsummary CCsummary,DNEA-method
Identify metabolic modules within the biological networks using a consensus clustering approachclusterNet
collapsed_DNEAcollapsed_DNEA collapsed_DNEA-class
consensusClusteringResultsconsensusClusteringResults consensusClusteringResults-class
Initialize a DNEA objectcreateDNEAobject
Access the dataset_summary slot of a DNEA objectdatasetSummary datasetSummary,DNEA-method
Retrieve the diagnostic values for the input expression datadiagnostics diagnostics,DNEA-method diagnostics,DNEAinputSummary-method
DNEA objectDNEA-class show,DNEA-method
DNEAinputSummaryDNEAinputSummary DNEAinputSummary-class show,DNEAinputSummary-method
Example results for DNEAdnw
Access the edge listedgeList 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 conditionsfilterNetworks filterNetworks,DNEA-method filterNetworks,list-method
Save network information to .csv filesgetNetworkFiles
Construct the GLASSO-based biological NetworksgetNetworks
Add additional metadata to the DNEA objectincludeMetadata
Access the lambda values tested during hyper parameter optimizationlambdas2Test lambdas2Test,DNEA-method
Initialize a DNEA object from a mass_dataset objectmassDataset2DNEA
Feature meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trialmetab_data
Retrieve metadata stored in a DNEAmetaData metaData,DNEA-method
Access the netGSA slot of a DNEA objectnetGSAresults netGSAresults,DNEA-method
Access and set the experimental group labelsnetworkGroupIDs networkGroupIDs,DNEA-method networkGroupIDs<-
Retrieve the unique group values of the experimental conditionnetworkGroups networkGroups,DNEA-method
Access the node listnodeList nodeList,DNEA-method nodeList<- nodeList<-,DNEA-method
Retrieve the total number of features in the datasetnumFeatures numFeatures,DNEA-method numFeatures,DNEAinputSummary-method
Retrieves the total number of samples in the datasetnumSamples numSamples,DNEA-method numSamples,DNEAinputSummary-method
Access the lambda value used in analysisoptimizedLambda optimizedLambda,DNEA-method optimizedLambda<- optimizedLambda<-,DNEA-method
Visualize the biological networksplotNetworks
Return the name of the current experimentprojectName projectName,DNEA-method
Identify metabolic modules that are enriched across experimental conditions using NetGSArunNetGSA
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 datastabilitySelection
Retrieve the subnetwork membership for each featuresubnetworkMembership subnetworkMembership,consensusClusteringResults-method subnetworkMembership,DNEA-method
Initialize a DNEA from SummarizedExperimentsumExp2DNEA
Sample meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trialT1Dmeta
Example expresion data set from The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trialTEDDY