GeDi (development version) (original) (raw)

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

Defining and visualizing the distances between different genesets

Bioconductor version: Development (3.22)

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] ORCID iD ORCID: 0000-0002-2475-4945 , Federico Marini [aut] ORCID iD ORCID: 0000-0003-3252-7758

Maintainer: Annekathrin Nedwed

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

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("GeDi")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Details

biocViews Clustering, GO, GUI, GeneSetEnrichment, KEGG, Pathways, RNASeq, Reactome, ReportWriting, ShinyApps, Software, Transcription, Visualization
Version 1.5.0
In Bioconductor since BioC 3.19 (R-4.4) (1 year)
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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Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/GeDi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GeDi
Package Short Url https://bioconductor.org/packages/GeDi/
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