Package: iNETgrate 1.5.0
Habil Zare
iNETgrate: Integrates DNA methylation data with gene expression in a single gene network
The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.
Authors:
iNETgrate_1.5.0.tar.gz
iNETgrate_1.5.0.zip(r-4.5)iNETgrate_1.5.0.zip(r-4.4)
iNETgrate_1.5.0.tgz(r-4.4-any)
iNETgrate_1.5.0.tar.gz(r-4.5-noble)iNETgrate_1.5.0.tar.gz(r-4.4-noble)
iNETgrate_1.5.0.tgz(r-4.4-emscripten)
iNETgrate.pdf |iNETgrate.html✨
iNETgrate/json (API)
NEWS
| # Install 'iNETgrate' in R: |
| install.packages('iNETgrate', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/biocmanager/issues
- toyCleanedAml - A subset of cleaned TCGA-LAML data
- toyComputEloci - A subset of weighted DNA methylation profile of TCGA-LAML data
- toyEigengenes - A subset of weighted average of gene expression present in each module
- toyRawAml - A subset of TCGA-LAML data
On BioConductor:iNETgrate-1.3.0(bioc 3.20)iNETgrate-1.2.0(bioc 3.19)
geneexpressionrnaseqdnamethylationnetworkinferencenetworkgraphandnetworkbiomedicalinformaticssystemsbiologytranscriptomicsclassificationclusteringdimensionreductionprincipalcomponentmrnamicroarraynormalizationgenepredictionkeggsurvivalcore-services
Last updated 23 days agofrom:4216302a77. Checks:OK: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | OK | Oct 31 2024 |
| R-4.5-linux | OK | Oct 30 2024 |
| R-4.4-win | OK | Oct 31 2024 |
| R-4.4-mac | OK | Oct 31 2024 |
Exports:accelFailAnalysisanalyzeSurvivalbestInetgratorcleanAllDatacomputEigengenescomputEigenlocicomputeInetgratorcomputeUnioncoxAnalysiscreateLocusGenedistanceToTsselectGenesfilterLowCorfindAliveCutofffindCorefindTcgaDuplicatesiNETgrateinferEigengenesmakeNetworkplotKMplotLociNumplotLociTssprepareSurvivalpreprocessDnamsample2patsampleData
Dependencies:abindannotateAnnotationDbiapeaplotaskpassbackportsbase64base64encbeanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocStylebiomaRtBiostringsbitbit64bitopsblobbnlearnbookdownbslibbumphunterC50cachemcaretcaToolscheckmateclassclicliprclockclusterclusterProfilercodetoolscolorspacecowplotcpp11crayonCubistcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdiagramdigestdoParalleldoRNGDOSEdplyrdynamicTreeCute1071enrichplotevaluatefansifarverfastclusterfastmapfastmatchfgseafilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsfuturefuture.applygdatagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtangleggtreeglmnetglobalsglueGO.dbGOSemSimgowergplotsgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablegtoolshardhatHDF5ArrayhighrHmischmsHomo.sapienshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphilluminaioimputeinumipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelavalazyevallibcoinlifecyclelimmalistenvlocfitlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemgcvmimeminfiModelMetricsmulttestmunsellmvtnormnlmennetnor1mixnumDerivopensslopenxlsxorg.Hs.eg.dbOrganismDbiparallellypartykitpatchworkpheatmapPigengenepillarpkgconfigplogrplyrpngpolyclippreprocessCoreprettyunitspROCprodlimprogressprogressrproxypurrrquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratRCurlreactome.dbReactomePAreadrrecipesrentrezreshapereshape2restfulrRfastRgraphvizrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorssassscalesscatterpiescrimeselectrshapesiggenessnowSparseArraysparseMatrixStatsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttidytreetimechangetimeDatetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg19.knownGenetxdbmakertzdbUCSC.utilsutf8vctrsviridisviridisLitevroomWGCNAwithrxfunXMLxml2xtableXVectoryamlyulab.utilszipzlibbioc
