gINTomics

This is the development version of gINTomics; for the stable release version, see gINTomics.

Multi-Omics data integration


Bioconductor version: Development (3.20)

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] , Francesco Patane' [aut] , Chiara Romualdi [aut]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("gINTomics")

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

Documentation

Reference Manual PDF

Details

biocViews CopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization
Version 1.1.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
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
System Requirements
URL https://github.com/angelovelle96/gINTomics
Bug Reports https://github.com/angelovelle96/gINTomics/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/gINTomics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gINTomics
Package Short Url https://bioconductor.org/packages/gINTomics/
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