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gINTomics

Multi-Omics data integration

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gINTomics")

Details

MaintainerAngelo Velle <angelo.velle@unipd.it>
AuthorAngelo Velle [cre, aut] (ORCID: <https://orcid.org/0000-0002-4010-6390>), Francesco Patane' [aut] (ORCID: <https://orcid.org/0009-0001-8619-447X>), Chiara Romualdi [aut] (ORCID: <https://orcid.org/0000-0003-4792-9047>)
LicenseAGPL-3
URLhttps://github.com/angelovelle96/gINTomics
Bug Reportshttps://github.com/angelovelle96/gINTomics/issues
Downloads rank158
Source branchRELEASE_3_23
biocViewsCopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization

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Dependencies

Depends: R (>= 4.4.0)

Imports: BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges, gtools, MultiAssayExperiment, plyr, stringi, stringr, SummarizedExperiment, methods, stats, reshape2, randomForest, limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics, GenomicFeatures, ReactomePA, clusterProfiler, dplyr, AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges, ggtree, shinydashboard, plotly, DT, MASS, InteractiveComplexHeatmap, ComplexHeatmap, visNetwork, shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr, circlize, MethylMix, shinyjs

Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)