Package: GeDi 1.9.0

Annekathrin Nedwed

GeDi: Defining and visualizing the distances between different genesets

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.

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

GeDi_1.9.0.tar.gz
GeDi_1.9.0.zip(r-4.7)GeDi_1.9.0.zip(r-4.6)GeDi_1.9.0.zip(r-4.5)
GeDi_1.9.0.tgz(r-4.6-any)GeDi_1.9.0.tgz(r-4.5-any)
GeDi_1.9.0.tar.gz(r-4.7-any)GeDi_1.9.0.tar.gz(r-4.6-any)
GeDi_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeDi/json (API)

# Install 'GeDi' in R:

install.packages('GeDi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/annekathrinsilvia/gedi/issues

Datasets:

macrophage_KEGG_example - A sample input RData file
macrophage_Reactome_example - A sample input RData file
macrophage_topGO_example - A sample input RData file
macrophage_topGO_example_small - A small sample input RData file
ppi_macrophage_topGO_example_small - PPI
sample_geneset - A sample input text file
sample_geneset_broken - A broken input text file
sample_geneset_empty - An empty input text file
sample_geneset_small - A small sample input text file
scores_macrophage_topGO_example_small - Sample scores

On BioConductor:GeDi-1.9.0(bioc 3.24)GeDi-1.7.1(bioc 3.23)

gui genesetenrichment software transcription rnaseq visualization clustering pathways reportwriting go kegg reactome shinyapps

5.96 score 2 stars 76 scripts 38 exports 159 dependencies

Last updated from:286938904b. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	361
linux-devel-x86_64	ERROR	656
source / vignettes	OK	538
linux-release-x86_64	ERROR	654
macos-release-arm64	ERROR	574
macos-oldrel-arm64	ERROR	346
windows-devel	ERROR	567
windows-release	ERROR	579
windows-oldrel	ERROR	578
wasm-release	OK	381

Exports:.cluster_markov .map_to_color buildClusterGraph buildGraph buildHistogramData checkInclusion clustering distanceDendro distanceHeatmap enrichmentWordcloud fuzzyClustering GeDi getAdjacencyMatrix getAnnotation getBipartiteGraph getClusterAdjacencyMatrix getGenes getGraphTitle getId getInteractionScore getJaccardMatrix getKappaMatrix getMeetMinMatrix getpMMMatrix getPPI getSorensenDiceMatrix getStringDB goDistance gsHistogram kMeansClustering kNN_clustering louvainClustering markovClustering pamClustering path_to_GeDi pMMlocal prepareGenesetData seedFinding

Dependencies:abind askpass assorthead base64enc beachmat BH BiocFileCache BiocGenerics BiocNeighbors BiocParallel bit bit64 bitops blob bs4Dash bslib cachem caTools cellranger chron circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest doParallel dplyr DT evaluate expm farver fastmap fastmatch filelock fontawesome foreach formatR fresh fs futile.logger futile.options generics GetoptLong ggdendro ggplot2 GlobalOptions glue gplots gsubfn gtable gtools hash highr hms htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime NLP openssl otel pillar pkgconfig plotly plotrix plyr png Polychrome prettyunits progress promises proto proxyC purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo readxl rematch rintrojs rjson rlang rmarkdown RSQLite rstudioapi S4Arrays S4Vectors S7 sass scales scatterplot3d shape shiny shinyBS shinycssloaders shinyWidgets simona slam snow sourcetools SparseArray sqldf STRINGdb stringi stringr sys tibble tidyr tidyselect tinytex tm utf8 vctrs viridisLite visNetwork waiter withr wordcloud2 xfun xml2 xtable XVector yaml

The GeDi User's Guide

Rendered fromGeDi_manual.Rmdusingknitr::rmarkdown

Last update: 2025-11-12
Started: 2022-02-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check genesets format	.checkGenesets
Check GeneTonic List format	.checkGTL
Check PPI format	.checkPPI
Check distance scores format	.checkScores
Markov Clustering (MCL) for community detection	.cluster_markov
Filter Genesets from the input data	.filterGenesets
Make an educated guess on the separator character	.findSeparator
Map each geneset to the cluster it belongs	.getClusterDatatable
Get gene set descriptions	.getGenesetDescriptions
Determine the number of cores to use for a function	.getNumberCores
Generate a 'data.frame' of graph metrics	.graphMetricsGenesetsDT
Maps numeric values to color values	.map_to_color
Make an educated guess on the separator character	.sepguesser
Build a cluster graph	buildClusterGraph
Construct a graph	buildGraph
Prepare data for 'gsHistogram()'.	buildHistogramData
Check for subset inclusion	checkInclusion
Cluster genesets.	clustering
Deprecated functions in GeDi	deprecated
Plot a dendrogram	distanceDendro
Plot a heatmap	distanceHeatmap
Visualize the results of an enrichment analysis as word cloud	enrichmentWordcloud
Find cluster from initial seeds	fuzzyClustering
GeDi main function	GeDi
Construct an adjacency matrix	getAdjacencyMatrix
Get the annotation of a 'STRINGdb' object	getAnnotation
Construct a bipartite graph	getBipartiteGraph
Construct an adjacency matrix	getClusterAdjacencyMatrix
Split string of genes	getGenes
Build up the node title	getGraphTitle
Get NCBI ID	getId
Calculate interaction score for two genesets	getInteractionScore
Get Matrix of Jaccard distances	getJaccardMatrix
Get Matrix of Kappa distances	getKappaMatrix
Get Matrix of Meet-Min distances	getMeetMinMatrix
Calculate the pMM distance	getpMMMatrix
Download Protein-Protein Interaction (PPI)	getPPI
Get Matrix of Sorensen-Dice distances	getSorensenDiceMatrix
Get the STRING db entry of a species	getStringDB
Calculate similarity of GO terms	goDistance
Create a histogram plot for gene set sizes	gsHistogram
Calculate clusters based on kMeans clustering	kMeansClustering
Calculate clusters based on kNN clustering	kNN_clustering
Cluster genesets using Louvain clustering.	louvainClustering
A sample input RData file	macrophage_KEGG_example
A sample input RData file	macrophage_Reactome_example
A sample input RData file	macrophage_topGO_example
A small sample input RData file	macrophage_topGO_example_small
Cluster genesets using Markov clustering.	markovClustering
Calculate clusters based on PAM clustering	pamClustering
Prepare enrichment analysis output data for GeDi	path_to_GeDi
Calculate local pMM distance	pMMlocal
PPI	ppi_macrophage_topGO_example_small
Split string of genes	prepareGenesetData
A sample input text file	sample_geneset
A broken input text file	sample_geneset_broken
An empty input text file	sample_geneset_empty
A small sample input text file	sample_geneset_small
Sample scores	scores_macrophage_topGO_example_small
Find clustering seeds	seedFinding