GeDi

This is the development version of GeDi; for the stable release version, see GeDi.

Defining and visualizing the distances between different genesets


Bioconductor version: Development (3.20)

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.

Author: Annekathrin Nedwed [aut, cre] , Federico Marini [aut]

Maintainer: Annekathrin Nedwed <anneludt at uni-mainz.de>

Citation (from within R, enter citation("GeDi")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GeDi")

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("GeDi")
The GeDi User's Guide HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, GO, GUI, GeneSetEnrichment, KEGG, Pathways, RNASeq, Reactome, ReportWriting, ShinyApps, Software, Transcription, Visualization
Version 1.1.2
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4.0)
Imports GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache, cluster, circlize
System Requirements
URL https://github.com/AnnekathrinSilvia/GeDi
Bug Reports https://github.com/AnnekathrinSilvia/GeDi/issues
See More
Suggests knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools, pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db
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Package Archives

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

Source Package GeDi_1.1.2.tar.gz
Windows Binary GeDi_1.1.2.zip
macOS Binary (x86_64) GeDi_1.1.2.tgz
macOS Binary (arm64) GeDi_1.1.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/GeDi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeDi
Bioc Package Browser https://code.bioconductor.org/browse/GeDi/
Package Short Url https://bioconductor.org/packages/GeDi/
Package Downloads Report Download Stats