GeDi

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

Defining and visualizing the distances between different genesets

Bioconductor version: 3.19

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, GO, GUI, GeneSetEnrichment, KEGG, Pathways, RNASeq, Reactome, ReportWriting, ShinyApps, Software, Transcription, Visualization

Version 1.0.1

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

System Requirements

URL https://github.com/AnnekathrinSilvia/GeDi

Bug Reports https://github.com/AnnekathrinSilvia/GeDi/issues

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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Build Report Build Report

Package Archives

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

Source Package GeDi_1.0.1.tar.gz

Windows Binary (x86_64) GeDi_1.0.1.zip

macOS Binary (x86_64) GeDi_1.0.1.tgz

macOS Binary (arm64) GeDi_1.0.1.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

Old Source Packages for BioC 3.19 Source Archive