Package index

Workflow

Cluster and label gene sets.

geneSetSimplifyR()

Run the geneSetSimplifyR workflow

initializeList()

Initialize gene sets list

clusterGeneSets()

Cluster gene sets

labelClusters()

Label clusters in clustered gene sets list object

Visualization

plotBarchart()

Plot clusters as a bar chart

plotClusterLabels()

Plot label information for a particular cluster

plotClustree()

Plot cluster tree

plotDendrogram()

Plot dendrogram of cluster averages

plotEnrichments()

Plot enrichment as lollipop plot

plotHeatmap()

Plot enrichment as heatmap

plotProportions()

Plot proportions of gene sets in each cluster for each source

plotUMAP()

Scatter plot of UMAP dimensionality reduction

plotViolin()

Violin plot of clustering

Results and resolution

extractTable()

Extract summary table of clustering

extractResolution()

Extract the resolution currently used by default

updateResolution()

Update default resolution of gsList

updateClusterLabels()

Rename a cluster

normalizeClusterLevels()

Normalize cluster factor level order in a clustered gsList

Input helpers

Convert enrichment results and fetch gene sets.

parseFgsea()

Parse fgsea results into geneSetSimplifyR input

parsePairedGSEA()

Parse pairedGSEA results into geneSetSimplifyR input

getGeneSets()

Fetch MSigDB gene sets by pathway name

Clustering methods

Use or add community-detection methods for the SNN graph.

listClusterMethods()

List the available clustering methods

getClusterMethod()

Resolve a clustering method specification

clusterMethod()

Define a clustering method for clusterGeneSets()

registerClusterMethod()

Register a clustering method for use by name

snnToIgraph()

Convert an SNN graph to an igraph object

snnToMatrix()

Convert an SNN graph to a dense similarity matrix

Classes and data

show(<gsList>)

The gsList class

exampleGeneSets

Example Gene Sets

exampleEnrichment

Example Enrichment Results

exampleGsList

Example clustered and labeled gene sets

stopWords

Stop Words