gINTomics

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

Multi-Omics data integration

Bioconductor version: Development (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: ), Francesco Patane' [aut] (ORCID: ), Chiara Romualdi [aut] (ORCID: )

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")

# 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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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

Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	gINTomics_1.3.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/gINTomics/
Package Short Url	https://bioconductor.org/packages/gINTomics/
Package Downloads Report	Download Stats