Package: gINTomics 1.8.0

Angelo Velle

gINTomics: Multi-Omics data integration

gINTomics is an R package for Multi-Omics data integration and visualization. gINTomics is designed to detect the association between the expression of a target and of its regulators, taking into account also their genomics modifications such as Copy Number Variations (CNV) and methylation. What is more, gINTomics allows integration results visualization via a Shiny-based interactive app.

Authors:Angelo Velle [cre, aut], Francesco Patane' [aut], Chiara Romualdi [aut]

gINTomics_1.8.0.tar.gz
gINTomics_1.8.0.zip(r-4.7)gINTomics_1.8.0.zip(r-4.6)gINTomics_1.8.0.zip(r-4.5)
gINTomics_1.8.0.tgz(r-4.6-any)gINTomics_1.8.0.tgz(r-4.5-any)
gINTomics_1.8.0.tar.gz(r-4.7-any)gINTomics_1.8.0.tar.gz(r-4.6-any)
gINTomics_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gINTomics/json (API)
NEWS

# Install 'gINTomics' in R:
install.packages('gINTomics', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/angelovelle96/gintomics/issues

Datasets:
  • mirna_hsa - MiRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).
  • mmultiassay_ov - Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.

On BioConductor:gINTomics-1.9.0(bioc 3.24)gINTomics-1.8.0(bioc 3.23)

geneexpressionrnaseqmicroarrayvisualizationcopynumbervariationgenetargetquarto

5.08 score 3 stars 4 scripts 202 downloads 18 exports 237 dependencies

Last updated from:a84669e2e7 (on RELEASE_3_23). Checks:5 NOTE, 2 OK, 3 WARNING. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE450
linux-devel-x86_64NOTE811
source / vignettesOK594
linux-release-x86_64NOTE809
macos-release-arm64NOTE752
macos-oldrel-arm64NOTE579
windows-develWARNING946
windows-releaseWARNING825
windows-oldrelWARNING755
wasm-releaseOK382

Exports:create_multiassaydot_plotlyextract_model_resplot_chr_distributionplot_heatmapplot_networkplot_ridgeplot_tf_distributionplot_vennplot_volcanorun_cnv_integrationrun_genomic_enrichrun_genomic_integrationrun_met_integrationrun_multiomicsrun_shinyrun_tf_enrichrun_tf_integration

Dependencies:abindaisdkAnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcallrcellrangercheckmatecigarillocirclizeclicliprclisymbolsclueclusterclusterProfilercodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdir.expirydoParallelDOSEdplyrDTedgeRenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggridgesggtangleggtreeggvennGlobalOptionsglueGO.dbGOSemSimgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphimputeInteractiveComplexHeatmapIRangesisobanditeratorsjquerylibjsonlitekableExtraKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitloggerlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseMethylMixmimeMultiAssayExperimentnlmeOmnipathRopensslorg.Hs.eg.dborg.Mm.eg.dbotelpatchworkpillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqvalueR.matlabR.methodsS3R.ooR.utilsR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRCurlreactome.dbReactomePAreadrreadxlrematchreshape2restfulrRhtslibrjsonrlangrmarkdownRPMMRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesscatterpieselectrSeqinfosessioninfoshapeshinyshiny.goslingshiny.reactshinydashboardshinyjssnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsvglitesyssystemfontstextshapingtibbletidydrtidygraphtidyrtidyselecttidytreetimechangetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg38.knownGeneTxDb.Mmusculus.UCSC.mm10.knownGenetzdbutf8vctrsviridisviridisLitevisNetworkvroomwithrxfunXMLxml2xtableXVectoryamlyulab.utilszip

gINTomics vignette

Angelo Velle, Francesco Patanè, Chiara Romualdi

Rendered fromgINTomics.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2024-04-04
Started: 2023-07-18

Readme and manuals

Help Manual

Help pageTopics
MultiAssayExperiment generationcreate_multiassay
plotting enrichmentdot_plotly
Setting method for extracting resultsextract_model_res extract_model_res,list-method extract_model_res,MultiClass-method extract_model_res,MultiOmics-method
miRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).mirna_hsa
Example data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.mmultiassay_ov
MultiClass ClassMultiClass-class
MultiOmics ClassMultiOmics-class
plotting chr distributionplot_chr_distribution
plotting heatmapplot_heatmap
Plotting networkplot_network
plotting ridgeplot_ridge
plotting TF distributionplot_tf_distribution
plotting vennplot_venn
plotting volcanoplot_volcano
Integration of expression and Copy Number Variationsrun_cnv_integration
Running genomic enrichment analysisrun_genomic_enrich
Integration of expression, Copy Number Variations and methylation datarun_genomic_integration
Integration of expression and methylationrun_met_integration
Complete Multi-Omics integrationrun_multiomics
Start a Shiny application for integrated multi-omics data analysis.run_shiny
Running TF enrichment analysisrun_tf_enrich
Integration of expression and Transcription Factors / Generic Regulatorsrun_tf_integration