Package: qpgraph 2.47.1
Robert Castelo
qpgraph: Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
Estimate gene and eQTL networks from high-throughput expression and genotyping assays.
Authors:
qpgraph_2.47.1.tar.gz
qpgraph_2.47.1.zip(r-4.7)qpgraph_2.47.1.zip(r-4.6)qpgraph_2.47.1.zip(r-4.5)
qpgraph_2.47.1.tgz(r-4.6-x86_64)qpgraph_2.47.1.tgz(r-4.6-arm64)qpgraph_2.47.1.tgz(r-4.5-x86_64)qpgraph_2.47.1.tgz(r-4.5-arm64)
qpgraph_2.47.1.tar.gz(r-4.7-arm64)qpgraph_2.47.1.tar.gz(r-4.7-x86_64)qpgraph_2.47.1.tar.gz(r-4.6-arm64)qpgraph_2.47.1.tar.gz(r-4.6-x86_64)
qpgraph_2.47.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
qpgraph/json (API)
NEWS
| # Install 'qpgraph' in R: |
| install.packages('qpgraph', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rcastelo/qpgraph/issues
- filtered.regulon6.1 - Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
- gds680.eset - Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
- subset.filtered.regulon6.1 - Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
- subset.gds680.eset - Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
On BioConductor:qpgraph-2.47.0(bioc 3.24)qpgraph-2.46.0(bioc 3.23)
microarraygeneexpressiontranscriptionpathwaysnetworkinferencegraphandnetworkgeneregulationgeneticsgeneticvariabilitysnpsoftwareopenblas
Last updated from:947872c722. Checks:1 ERROR, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 244 | ||
| linux-devel-arm64 | OK | 391 | ||
| linux-devel-x86_64 | OK | 417 | ||
| source / vignettes | OK | 427 | ||
| linux-release-arm64 | OK | 388 | ||
| linux-release-x86_64 | OK | 437 | ||
| macos-release-arm64 | OK | 483 | ||
| macos-release-x86_64 | OK | 587 | ||
| macos-oldrel-arm64 | OK | 301 | ||
| macos-oldrel-x86_64 | OK | 420 | ||
| windows-devel | OK | 370 | ||
| windows-release | OK | 379 | ||
| windows-oldrel | OK | 351 | ||
| wasm-release | OK | 175 |
Exports:addeQTLaddGeneAssociationaddGenesalleQTLallGeneAssociationsciseQTLdetdeterminantdRegularGraphParamdRegularMarkedGraphParameQTLcrosseQTLcrossParameQTLnetworkEstimateeQTLnetworkEstimationParamerGraphParamerMarkedGraphParamfilterCollinearitiesgeneAnnotationgeneNamesgeneticMapggDatagraphHMgmmmarkerNamesphysicalMapplotqpAllCItestsqpAnyGraphqpAvgNrrqpBoundaryqpCItestqpCliqueqpCliqueNumberqpCovqpEdgeCorqpEdgeNrrqpFunctionalCoherenceqpG2SigmaqpGenNrrqpGetCliquesqpGraphqpGraphDensityqpHistqpHTFqpImportNrrqpIPFqpK2ParCorqpNrrqpPACqpPathWeightqpPCCqpPlotMapqpPlotNetworkqpPrecisionRecallqpPRscoreThresholdqpRndGraphqpRndWishartqpTopPairsqpUnifRndAssociationqpUpdateCliquesRemovingrcmvnormreQTLcrossresetCutoffsrgraphBAMrHMgmmrmvnormrUGgmmshowsim.crosssummarytranseQTLUGgmmvarExplained
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphhttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormopensslpkgconfigpngqtlR6RCurlrestfulrRgraphvizRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysvctrsXMLxtableXVectoryaml
Estimate eQTL networks using qpgraph
Rendered fromeQTLnetworks.Rnwusingutils::Sweaveon Jun 10 2026.Last update: 2025-07-23
Started: 2014-10-10
Reverse-engineer transcriptional regulatory networks using qpgraph
Rendered fromqpTxRegNet.Rnwusingutils::Sweaveon Jun 10 2026.Last update: 2014-02-04
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Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Estimation of genetic and molecular regulatory networks from high-throughput genomics data | qpgraph-package qpgraph |
| Preprocessed microarray oxygen deprivation data and filtered RegulonDB data | EcoliOxygen filtered.regulon6.1 gds680.eset subset.filtered.regulon6.1 subset.gds680.eset |
| eQTL experimental cross model class | $,eQTLcross-method addeQTL addeQTL,eQTLcross-method addGeneAssociation addGeneAssociation,eQTLcross-method addGenes addGenes,eQTLcross,integer-method addGenes,eQTLcross,missing-method addGenes,eQTLcross,numeric-method alleQTL,eQTLcross-method ciseQTL,eQTLcross,missing-method ciseQTL,eQTLcross,numeric-method eQTLcross eQTLcross,map,matrix,graphBAM-method eQTLcross,map,matrix,HMgmm-method eQTLcross,map,matrix,matrix-method eQTLcross,map,missing,HMgmm-method eQTLcross,map,missing,matrix-method eQTLcross,map,missing,missing-method eQTLcross-class eQTLcrossParam eQTLcrossParam-class geneNames,eQTLcross-method markerNames,eQTLcross-method names,eQTLcross-method plot,eQTLcross,ANY-method reQTLcross reQTLcross,eQTLcross,missing-method reQTLcross,eQTLcrossParam,missing-method reQTLcross,integer,eQTLcross-method reQTLcross,integer,eQTLcrossParam-method reQTLcross,missing,eQTLcross-method reQTLcross,missing,eQTLcrossParam-method reQTLcross,numeric,eQTLcross-method reQTLcross,numeric,eQTLcrossParam-method show,eQTLcross-method show,eQTLcrossParam-method sim.cross sim.cross,map,eQTLcross-method sim.cross,map,matrix-method transeQTL transeQTL,eQTLcross,missing-method transeQTL,eQTLcross,numeric-method |
| eQTL network model class | alleQTL alleQTL,eQTLnetwork-method allGeneAssociations allGeneAssociations,eQTLnetwork-method ciseQTL ciseQTL,eQTLnetwork,missing-method ciseQTL,eQTLnetwork,numeric-method eQTLnetwork eQTLnetwork-class geneAnnotation,eQTLnetwork-method geneNames,eQTLnetwork-method geneticMap,eQTLnetwork-method graph graph,eQTLnetwork-method markerNames,eQTLnetwork-method physicalMap,eQTLnetwork-method plot,eQTLnetwork,ANY-method resetCutoffs resetCutoffs,eQTLnetwork-method show,eQTLnetwork-method varExplained varExplained,eQTLnetworkEstimationParam,eQTLnetwork-method |
| Estimation of a eQTL network from genetical genomics data | eQTLnetworkEstimate eQTLnetworkEstimate,eQTLnetworkEstimationParam,formula,eQTLnetwork-method eQTLnetworkEstimate,eQTLnetworkEstimationParam,formula,missing-method eQTLnetworkEstimate,eQTLnetworkEstimationParam,missing,eQTLnetwork-method |
| eQTL network parameter model class | eQTLnetworkEstimationParam eQTLnetworkEstimationParam-class geneAnnotation geneAnnotation,eQTLnetworkEstimationParam-method geneNames geneNames,eQTLnetworkEstimationParam-method geneticMap geneticMap,eQTLnetworkEstimationParam-method ggData ggData,eQTLnetworkEstimationParam-method markerNames markerNames,eQTLnetworkEstimationParam-method physicalMap physicalMap,eQTLnetworkEstimationParam-method show,eQTLnetworkEstimationParam-method |
| Filter collinearities | filterCollinearities |
| Graph parameter classes | dRegularGraphParam dRegularGraphParam-class dRegularMarkedGraphParam dRegularMarkedGraphParam-class erGraphParam erGraphParam-class erMarkedGraphParam erMarkedGraphParam-class graphParam-class markedGraphParam-class plot,graphBAM,ANY-method rgraphBAM rgraphBAM,dRegularGraphParam,missing-method rgraphBAM,erGraphParam,missing-method rgraphBAM,graphParam,missing-method rgraphBAM,integer,dRegularGraphParam-method rgraphBAM,integer,erGraphParam-method rgraphBAM,integer,graphParam-method rgraphBAM,missing,dRegularGraphParam-method rgraphBAM,missing,erGraphParam-method rgraphBAM,missing,graphParam-method rgraphBAM,numeric,dRegularGraphParam-method rgraphBAM,numeric,erGraphParam-method rgraphBAM,numeric,graphParam-method show,graphParam-method |
| Homogeneous mixed graphical Markov model | $,HMgmm-method dim,HMgmm-method dimnames,HMgmm-method HMgmm HMgmm,graphBAM-method HMgmm,matrix-method HMgmm,missing-method HMgmm-class names,HMgmm-method plot,HMgmm,ANY-method rcmvnorm rcmvnorm,ANY,HMgmm-method rHMgmm rHMgmm,graphBAM,missing-method rHMgmm,integer,graphBAM-method rHMgmm,integer,markedGraphParam-method rHMgmm,integer,matrix-method rHMgmm,markedGraphParam,missing-method rHMgmm,matrix,missing-method rHMgmm,missing,graphBAM-method rHMgmm,missing,markedGraphParam-method rHMgmm,missing,matrix-method rHMgmm,numeric,graphBAM-method rHMgmm,numeric,markedGraphParam-method rHMgmm,numeric,matrix-method show,HMgmm-method show,HMgmmSummary-method summary,HMgmm-method |
| Tests of conditional independence | qpAllCItests qpAllCItests,matrix-method |
| A graph | qpAnyGraph |
| Average non-rejection rate estimation | qpAvgNrr qpAvgNrr,data.frame-method qpAvgNrr,ExpressionSet-method qpAvgNrr,matrix-method |
| Maximum boundary size of the resulting qp-graphs | qpBoundary |
| Conditional independence test | qpCItest qpCItest,cross-method qpCItest,data.frame-method qpCItest,ExpressionSet-method qpCItest,matrix-method qpCItest,SsdMatrix-method |
| Complexity of the resulting qp-graphs | qpClique |
| Clique number | qpCliqueNumber |
| Calculation of the sample covariance matrix | qpCov |
| Non-rejection rate estimation for a pair of variables | qpEdgeCor qpEdgeCor,matrix-method qpEdgeCor,UGgmm-method qpEdgeNrr qpEdgeNrr,data.frame-method qpEdgeNrr,ExpressionSet-method qpEdgeNrr,matrix-method qpEdgeNrr,SsdMatrix-method |
| Functional coherence estimation | qpFunctionalCoherence qpFunctionalCoherence,list-method qpFunctionalCoherence,lsCMatrix-method qpFunctionalCoherence,lspMatrix-method qpFunctionalCoherence,lsyMatrix-method qpFunctionalCoherence,matrix-method |
| Random covariance matrix | qpG2Sigma |
| Generalized non-rejection rate estimation | qpGenNrr qpGenNrr,data.frame-method qpGenNrr,ExpressionSet-method qpGenNrr,list-method qpGenNrr,matrix-method |
| Clique list | qpGetCliques |
| The qp-graph | $,qpGraph-method names,qpGraph-method qpGraph qpGraph,dspMatrix-method qpGraph,matrix-method qpGraph-class show,qpGraph-method |
| Densities of resulting qp-graphs | qpGraphDensity |
| Histograms of non-rejection rates | qpHist |
| Hastie Tibshirani Friedman iterative regression algorithm | qpHTF |
| Import non-rejection rates | qpImportNrr |
| Iterative proportional fitting algorithm | qpIPF |
| Partial correlation coefficients | qpK2ParCor |
| Non-rejection rate estimation | qpNrr qpNrr,cross-method qpNrr,data.frame-method qpNrr,ExpressionSet-method qpNrr,matrix-method |
| Estimation of partial correlation coefficients | qpPAC qpPAC,data.frame-method qpPAC,ExpressionSet-method qpPAC,matrix-method |
| Calculation of path weights | qpPathWeight qpPathWeight,dspMatrix-method qpPathWeight,matrix-method |
| Estimation of Pearson correlation coefficients | qpPCC qpPCC,data.frame-method qpPCC,ExpressionSet-method qpPCC,matrix-method |
| Plots a map of associated pairs | qpPlotMap |
| Plots a graph | qpPlotNetwork |
| Calculation of precision-recall curves | qpPrecisionRecall |
| Calculation of scores thresholds attaining nominal precision or recall levels | qpPRscoreThreshold |
| Undirected random d-regular graphs | qpRndGraph |
| Random Wishart distribution | qpRndWishart |
| Report pairs of variables | qpTopPairs |
| Uniformly random association values | qpUnifRndAssociation |
| Update clique list when removing one edge | qpUpdateCliquesRemoving |
| Sum of squares and deviations Matrices | det,SsdMatrix-method determinant,SsdMatrix,logical-method determinant,SsdMatrix,missing-method dim,SsdMatrix-method dimnames,SsdMatrix-method show,SsdMatrix-method SsdMatrix-class |
| Undirected Gaussian graphical Markov model | $,UGgmm-method dim,UGgmm-method dimnames,UGgmm-method names,UGgmm-method plot,UGgmm,ANY-method rmvnorm rmvnorm,integer,numeric-method rmvnorm,numeric,numeric-method rmvnorm,numeric,UGgmm-method rUGgmm rUGgmm,graphBAM,missing-method rUGgmm,graphParam,missing-method rUGgmm,integer,graphBAM-method rUGgmm,integer,graphParam-method rUGgmm,integer,matrix-method rUGgmm,matrix,missing-method rUGgmm,missing,graphBAM-method rUGgmm,missing,graphParam-method rUGgmm,missing,matrix-method rUGgmm,numeric,graphBAM-method rUGgmm,numeric,graphParam-method rUGgmm,numeric,matrix-method show,UGgmm-method show,UGgmmSummary-method summary,UGgmm-method UGgmm UGgmm,graphBAM-method UGgmm,matrix-method UGgmm,missing-method UGgmm-class |
