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_1.29.0.tgz(r-4.4-any)omicRexposome_1.29.0.tgz(r-4.3-any)
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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'))

Peer review:

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 203 downloads 2 mentions 11 exports 216 dependencies

Last updated 2 months agofrom:0f242165b8. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 25 2024
R-4.5-winNOTENov 25 2024
R-4.5-linuxNOTENov 25 2024
R-4.4-winNOTENov 25 2024
R-4.4-macNOTENov 25 2024
R-4.3-winOKNov 25 2024
R-4.3-macOKNov 25 2024

Exports:add_clsadd_expassociationcrossomicsgetIntegrationplotAssociationplotHitsplotIntegrationplotLambdatableHitstableLambda

Dependencies:abindade4annotateAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcalibratecarcarDatacaToolscheckmatecirclizeclicliprclueclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDerivdigestdoBydplyrDTedgeRellipseemmeansestimabilityevaluateFactoMineRfansifarverfastICAfastmapflashClustfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglmnetGlobalOptionsgluegmmgplotsgridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrimputeimputeLCMDIRangesisobandisvaiteratorsJADEjomojquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4lobstrlocfitlsrmade4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicemicrobenchmarkmimeminqamitmlmodelrmultcompViewMultiDataSetmunsellmvtnormnlmenloptrnnetnormnumDerivomicade4opensslordinalpanpbkrtestpcaMethodspillarpixmappkgconfigplogrplyrPMApngprettyunitsprogresspromisespryrpurrrqqmanquantregqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreshape2rexposomerlangrmarkdownrpartRSpectraRSQLiterstudioapiS4ArraysS4Vectorssandwichsassscalesscatterplot3dshapeSmartSVAsnowspSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytextmvtnormtzdbucminfUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioczoo

Exposome Data Integration with Omic Data

Carles Hernandez-Ferer and Juan R. Gonzalez

Rendered fromexposome_omic_integration.Rmdusingknitr::rmarkdownon Nov 25 2024.

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