Package: omicRexposome 1.29.0

Xavier Escribà Montagut

omicRexposome: Exposome and omic data associatin and integration analysis

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

Authors:Carles Hernandez-Ferrer [aut, cre], Juan R. González [aut]

omicRexposome_1.29.0.tar.gz
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omicRexposome.pdf |omicRexposome.html✨
omicRexposome/json (API)

# Install 'omicRexposome' in R:
install.packages('omicRexposome', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • asr - 'ResultSet' for testing and illustration purpouses
  • crs - 'ResultSet' for testing and illustration purpouses
  • mds - 'MultiDataSet' for testing and illustration purpouses

On BioConductor:omicRexposome-1.29.0(bioc 3.21)omicRexposome-1.28.0(bioc 3.20)

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

immunooncologyworkflowstepmultiplecomparisonvisualizationgeneexpressiondifferentialexpressiondifferentialmethylationgeneregulationepigeneticsproteomicstranscriptomicsstatisticalmethodregression

4.48 score 5 scripts 228 downloads 2 mentions 11 exports 218 dependencies

Last updated 4 months agofrom:0f242165b8. Checks:3 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 24 2025
R-4.5-winNOTEJan 24 2025
R-4.5-linuxNOTEJan 24 2025
R-4.4-winNOTEJan 24 2025
R-4.4-macNOTEJan 24 2025
R-4.3-winOKJan 24 2025
R-4.3-macOKJan 24 2025

Exports:add_clsadd_expassociationcrossomicsgetIntegrationplotAssociationplotHitsplotIntegrationplotLambdatableHitstableLambda

Dependencies:abindade4annotateAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcalibratecarcarDatacaToolscheckmatecirclizeclicliprclueclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDerivdigestdoBydplyrDTedgeRellipseemmeansestimabilityevaluateFactoMineRfansifarverfastICAfastmapflashClustfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglmnetGlobalOptionsgluegmmgplotsgridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrimputeimputeLCMDIRangesisobandisvaiteratorsJADEjomojquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4lobstrlocfitlsrmade4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicemicrobenchmarkmimeminqamitmlmodelrmultcompViewMultiDataSetmunsellmvtnormnlmenloptrnnetnormnumDerivomicade4opensslordinalpanpbkrtestpcaMethodspillarpixmappkgconfigplogrplyrPMApngprettyunitsprogresspromisespryrpurrrqqmanquantregqvalueR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasreshape2rexposomerlangrmarkdownrpartRSpectraRSQLiterstudioapiS4ArraysS4Vectorssandwichsassscalesscatterplot3dshapeSmartSVAsnowspSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytextmvtnormtzdbucminfUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxtableXVectoryamlzoo

Exposome Data Integration with Omic Data

Carles Hernandez-Ferer and Juan R. Gonzalez

Rendered fromexposome_omic_integration.Rmdusingknitr::rmarkdownon Jan 24 2025.

Last update: 2024-02-12
Started: 2017-03-31

Readme and manuals

Help Manual

Help pageTopics
Method to add an ExposomeClust to a MultiDataSetadd_cls add_cls,MultiDataSet,ExposomeClust-method
Method to add an ExposomeSet to a MultiDataSetadd_exp add_exp,MultiDataSet,ExposomeSet-method
'ResultSet' for testing and illustration purpousesasr
# -------------------------- Method to perform an association study between transcriptome and exposomassociation association,MultiDataSet-method
Function to perform a Transcriptome-Wide Association Studycrossomics crossomics,MultiDataSet-method
'ResultSet' for testing and illustration purpousescrs
Method to extrat integration-feature result from a ResultSetgetIntegration getIntegration,ResultSet-method
'MultiDataSet' for testing and illustration purpousesmds
omicRexposome: Package for exposome and omic data associatin and integrationomicRexposome-package omicRexposome
Function to draw de result of an association studyplotAssociation plotAssociation,ResultSet-method
Plot number of hits per result in ResultSetplotHits plotHits,ResultSet-method
Function to draw de result of an integration studyplotIntegration plotIntegration,ResultSet-method
Plot lambda score for all results in a ResultSetplotLambda plotLambda,ResultSet-method
Transforms the discrete genotype from a 'snpSet' to a 'matrix' of a continuous variable.snpToContinuous snpToContinuous,SnpSet-method
Counts the number of hits on the results stored in a ResultSettableHits tableHits,ResultSet-method
Compute a lambda score on the results stored in a ResultSettableLambda tableLambda,ResultSet-method