gINTomics

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see gINTomics.

Multi-Omics data integration

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

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

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 gINTomics_1.0.0.tar.gz

Windows Binary (x86_64) 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/

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