gINTomics

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

Multi-Omics data integration

Bioconductor version: Release (3.23)

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")):

Angelo Velle, Francesco Patane', Chiara Romualdi. gINTomics: Multi-Omics data integration. doi:10.18129/B9.bioc.gINTomics, R package version 1.8.0, https://bioconductor.org/packages/gINTomics.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

No vignettes available
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.19 (R-4.4) (2.5 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, MethylMix, shinyjs
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
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	gINTomics_1.8.0.tar.gz
Windows Binary (x86_64)	gINTomics_1.8.0.zip
macOS Binary (big-sur-x86_64)	gINTomics_1.8.0.tgz
macOS Binary (sonoma-arm64)	gINTomics_1.8.0.tgz
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/
Package Downloads Report	Download Stats