GeDi

Defining and visualizing the distances between different genesets

Bioconductor version: 3.23 · Package version: 1.8.0

The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GeDi")

Details

Maintainer	Annekathrin Nedwed <anneludt@uni-mainz.de>
Author	Annekathrin Nedwed [aut, cre] (ORCID: <https://orcid.org/0000-0002-2475-4945>), Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
License	MIT + file LICENSE
URL	https://github.com/AnnekathrinSilvia/GeDi
Bug Reports	https://github.com/AnnekathrinSilvia/GeDi/issues
Downloads rank	206
Source branch	RELEASE_3_23
biocViews	Clustering, GO, GUI, GeneSetEnrichment, KEGG, Pathways, RNASeq, Reactome, ReportWriting, ShinyApps, Software, Transcription, Visualization

Documentation

The GeDi User's Guide

Download

Source package

Dependencies

Depends: R (>= 4.4.0)

Imports: Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, expm, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache, cluster, methods, circlize, proxyC, simona

Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, mosdef, GeneTonic, htmltools, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db