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linkcomm (version 1.0-14)

Tools for Generating, Visualizing, and Analysing Link Communities in Networks

Description

Link communities reveal the nested and overlapping structure in networks, and uncover the key nodes that form connections to multiple communities. linkcomm provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and analysing Overlapping Cluster Generator (OCG) communities. Kalinka and Tomancak (2011) .

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Install

install.packages('linkcomm')

Monthly Downloads

164

Version

1.0-14

License

GPL (>= 2)

Issues

Pull Requests

Stars

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Maintainer

Alex T Kalinka

Last Published

February 4th, 2021

Functions in linkcomm (1.0-14)

edge.duplicates

Find and Remove Edge Loops and Duplicates
getAllNestedComm

Find Nested Communities
corLinkcommCentrality

Correlation of Community Centrality with Classic Centrality
get.shared.nodes

Get Nodes Shared by Communities
cutDendrogramAt

Extract Meta-Communities
get.community.overlaps

Find Node Overlaps between Communities
getCommunityCentrality

Calculate Community Centrality Measures for Nodes
LinkDensities

Calculate Link Community Link Densities
getClusterRelatedness

Hierarchichal Clustering of Link Communities
getLinkCommunities

Extract Link Communities from a Network
getCommunityMatrix

Construct a Community Membership Matrix
getOCG.clusters

Generate Overlapping Cluster Generator (OCG) Communities
getNodesIn

Extract Nodes from Communities
getEdgesIn

Extract Edge Indices from Communities
pp_rnapol

Sample Yeast Protein Interactome
plotOCGraph

Plot a Graph Layout of OCG Communities
meta.communities

Produce a Set of Meta-Communities
integer.edgelist

Convert A Network to an Integer Edgelist
linkcomm2cytoscape

Write an Edge Attribute File for Cytoscape
orderCommunities

Order Link Communities According to the Dendrogram
plot.OCG

The OCG Plotting Function
karate

Social Network in a Karate Club
newLinkCommsAt

User-Defined Link Communities
getCommunityConnectedness

Calculate Community Connectedness or Modularity
numberEdgesIn

Extract Node Community Membership by Edges
getNestedHierarchies

Find Nested Structures in Communities
lesmiserables

Co-Appearance Network from Les Miserables
layout.spencer.circle

Calculate Node Coordinates for a Spencer Circle
plotLinkCommSumm

Plot a Summary of the Link Community Algorithm Output
print.linkcomm

Print a Summary of a linkcomm Object
print.OCG

Print a Summary of an OCG Object
plotLinkCommSummComm

Plot a Summary of the Link Communities
which.communities

Extract Community Membership for Nodes
graph.feature

Make Node or Edge Graph Features
linkcomm-package

The linkcomm package
human_pp

Sample Human Protein Interactome
plotLinkCommDend

Plot a Coloured Dendrogram of Link Communities
read.OCG

Read an OCG Partition File into R
plot.linkcomm

The linkcomm Plotting Function
plotLinkCommGraph

Plot a Graph Layout of Link Communities
linkcomm2clustnsee

Write a Partition File for Clust&See
plotLinkCommMembers

Plot a Community Membership Matrix for Link Communities
weighted

Sample Gene Co-Expression Network