Defining and visualizing the distances between different genesets

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Documentation for package ‘GeDi’ version 1.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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