GeDi
Defining and visualizing the distances between different genesets
Bioconductor version: 3.23 · Package version: 1.7.1
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 | 318 |
| Source branch | RELEASE_3_23 |
| biocViews | Clustering, GO, GUI, GeneSetEnrichment, KEGG, Pathways, RNASeq, Reactome, ReportWriting, ShinyApps, Software, Transcription, Visualization |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | GeDi_1.7.1.tar.gz |
| Windows binary (x86_64) | GeDi_1.7.1.zip |
| macOS binary (arm64) | GeDi_1.7.1.tgz |
| macOS binary (x86_64) | GeDi_1.7.1.tgz |
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