Package: gINTomics 1.1.0

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_1.1.0.tar.gz
gINTomics_1.1.0.zip(r-4.5)gINTomics_1.1.0.zip(r-4.4)gINTomics_1.1.0.zip(r-4.3)
gINTomics_1.1.0.tgz(r-4.4-any)gINTomics_1.1.0.tgz(r-4.3-any)
gINTomics_1.1.0.tar.gz(r-4.5-noble)gINTomics_1.1.0.tar.gz(r-4.4-noble)
gINTomics_1.1.0.tgz(r-4.4-emscripten)gINTomics_1.1.0.tgz(r-4.3-emscripten)
gINTomics.pdf |gINTomics.html✨
gINTomics/json (API)
NEWS

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

Peer review:

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-1.1.0(bioc 3.20)gINTomics-1.0.0(bioc 3.19)

bioconductor-package

18 exports 2.00 score 227 dependencies

Last updated 2 months agofrom:c1c358f16a

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:abindAnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcachemcallrcellrangercheckmatecirclizeclicliprclisymbolsclueclusterclusterProfilercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdoParallelDOSEdownloaderdplyrDTedgeRenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggridgesggtreeggvennGlobalOptionsglueGO.dbGOSemSimgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablegtoolsHDO.dbhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphInteractiveComplexHeatmapIRangesisobanditeratorsjquerylibjsonlitekableExtraKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitloggerlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMultiAssayExperimentmunsellnlmeOmnipathRopensslorg.Hs.eg.dborg.Mm.eg.dbpatchworkpillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqvalueR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreactome.dbReactomePAreadrreadxlrematchreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4Vectorssassscalesscatterpieselectrshadowtextshapeshinyshiny.goslingshiny.reactshinydashboardsnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsvglitesyssystemfontstibbletidygraphtidyrtidyselecttidytreetimechangetinytextreeiotweenrTxDb.Hsapiens.UCSC.hg38.knownGeneTxDb.Mmusculus.UCSC.mm10.knownGenetzdbUCSC.utilsutf8vctrsviridisviridisLitevisNetworkvroomwithrxfunXMLxml2xtableXVectoryamlyulab.utilszlibbioc

gINTomics vignette

Angelo Velle, Francesco Patanè, Chiara Romualdi

Rendered fromgINTomics.Rmdusingknitr::rmarkdownon Jul 02 2024.

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