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:
Maintainer: Angelo Velle <angelo.velle at unipd.it>
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 | ||
| NEWS | Text |
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 |
See More
| 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) | gINTomics_1.3.0.zip |
| macOS Binary (x86_64) | gINTomics_1.3.0.tgz |
| macOS Binary (arm64) | gINTomics_1.3.0.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 |