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Bioconductor - gINTomics

gINTomics

This is the released version of gINTomics; for the devel version, see gINTomics.

Multi-Omics data integration

Bioconductor version: Release (3.21)

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.

Author: Angelo Velle [cre, aut] ORCID: 0000-0002-4010-6390 , Francesco Patane' [aut] ORCID: 0009-0001-8619-447X , Chiara Romualdi [aut] ORCID: 0000-0003-4792-9047

Maintainer: Angelo Velle <angelo.velle at unipd.it>

Citation (from within R, enter citation("gINTomics")): Installation

To install this package, start R (version "4.5") and enter:


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

BiocManager::install("gINTomics")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gINTomics")
Details biocViews CopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization Version 1.4.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License AGPL-3 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 System Requirements URL https://github.com/angelovelle96/gINTomics Bug Reports https://github.com/angelovelle96/gINTomics/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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