GeDi
Defining and visualizing the distances between different genesets
Bioconductor version: 3.24 · Package version: 1.9.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, GO, GUI, GeneSetEnrichment, KEGG, Pathways, RNASeq, Reactome, ReportWriting, ShinyApps, Software, Transcription, Visualization |
| Package Short Url | https://bioconductor.org/packages/GeDi/ |
Citation
From within R, enter citation("GeDi"):
Annekathrin Nedwed, Federico Marini. GeDi: Defining and visualizing the distances between different genesets. doi:10.18129/B9.bioc.GeDi, R package version 1.9.0, https://bioconductor.org/packages/GeDi.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
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