gINTomics

Multi-Omics data integration


Bioconductor version: Release (3.19)

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")

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")
gINTomics vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization
Version 1.0.0
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
See More
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package gINTomics_1.0.0.tar.gz
Windows Binary gINTomics_1.0.0.zip
macOS Binary (x86_64) gINTomics_1.0.0.tgz
macOS Binary (arm64) gINTomics_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/gINTomics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gINTomics
Bioc Package Browser https://code.bioconductor.org/browse/gINTomics/
Package Short Url https://bioconductor.org/packages/gINTomics/
Package Downloads Report Download Stats