gINTomics
Multi-Omics data integration
Bioconductor version: 3.23 · Package version: 1.8.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("gINTomics") Details
| Maintainer | Angelo Velle <angelo.velle@unipd.it> |
| Author | Angelo Velle [cre, aut] (ORCID: <https://orcid.org/0000-0002-4010-6390>), Francesco Patane' [aut] (ORCID: <https://orcid.org/0009-0001-8619-447X>), Chiara Romualdi [aut] (ORCID: <https://orcid.org/0000-0003-4792-9047>) |
| License | AGPL-3 |
| URL | https://github.com/angelovelle96/gINTomics |
| Bug Reports | https://github.com/angelovelle96/gINTomics/issues |
| Downloads rank | 158 |
| Source branch | RELEASE_3_23 |
| biocViews | CopyNumberVariation, GeneExpression, GeneTarget, Microarray, RNASeq, Software, Visualization |
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Dependencies
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
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)