Package: linkcomm 1.0-14

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

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) <doi:10.1093/bioinformatics/btr311>.

Authors:Alex T. Kalinka <[email protected]>, with contributions from Alain Guenoche

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linkcomm.pdf |linkcomm.html✨
linkcomm/json (API)
NEWS

# Install 'linkcomm' in R:
install.packages('linkcomm', repos = c('https://alextkalinka.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/alextkalinka/linkcomm/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • human_pp - Sample Human Protein Interactome
  • karate - Social Network in a Karate Club
  • lesmiserables - Co-Appearance Network from Les Miserables
  • pp_rnapol - Sample Yeast Protein Interactome
  • weighted - Sample Gene Co-Expression Network

On CRAN:

clusteringnetworksnetworks-biologyvisualization

33 exports 7 stars 2.72 score 13 dependencies 3 dependents 7 mentions 103 scripts 446 downloads

Last updated 4 years agofrom:b47d5e6018. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 26 2024
R-4.5-win-x86_64NOTEAug 26 2024
R-4.5-linux-x86_64NOTEAug 26 2024
R-4.4-win-x86_64OKAug 26 2024
R-4.4-mac-x86_64OKAug 26 2024
R-4.4-mac-aarch64OKAug 26 2024
R-4.3-win-x86_64OKAug 26 2024
R-4.3-mac-x86_64OKAug 26 2024
R-4.3-mac-aarch64OKAug 26 2024

Exports:corLinkcommCentralitycutDendrogramAtedge.duplicatesget.community.overlapsget.shared.nodesgetAllNestedCommgetClusterRelatednessgetCommunityCentralitygetCommunityConnectednessgetCommunityMatrixgetEdgesIngetLinkCommunitiesgetNestedHierarchiesgetNodesIngetOCG.clustersgraph.featureinteger.edgelistlayout.spencer.circlelinkcomm2clustnseelinkcomm2cytoscapeLinkDensitiesmeta.communitiesnewLinkCommsAtnumberEdgesInorderCommunitiesplotLinkCommDendplotLinkCommGraphplotLinkCommMembersplotLinkCommSummplotLinkCommSummCommplotOCGraphread.OCGwhich.communities

Dependencies:clicpp11dynamicTreeCutglueigraphlatticelifecyclemagrittrMatrixpkgconfigRColorBrewerrlangvctrs

R packages: Static PDF and HTML vignettes

Rendered fromlinkcomm.pdf.asisusingR.rsp::asison Aug 26 2024.

Last update: 2020-10-03
Started: 2020-10-03

Readme and manuals

Help Manual

Help pageTopics
The 'linkcomm' packagelinkcomm-package linkcomm
Correlation of Community Centrality with Classic CentralitycorLinkcommCentrality
Extract Meta-CommunitiescutDendrogramAt
Find and Remove Edge Loops and Duplicatesedge.duplicates
Find Node Overlaps between Communitiesget.community.overlaps
Get Nodes Shared by Communitiesget.shared.nodes
Find Nested CommunitiesgetAllNestedComm
Hierarchichal Clustering of Link CommunitiesgetClusterRelatedness
Calculate Community Centrality Measures for NodesgetCommunityCentrality
Calculate Community Connectedness or ModularitygetCommunityConnectedness
Construct a Community Membership MatrixgetCommunityMatrix
Extract Edge Indices from CommunitiesgetEdgesIn
Extract Link Communities from a NetworkgetLinkCommunities
Find Nested Structures in CommunitiesgetNestedHierarchies
Extract Nodes from CommunitiesgetNodesIn
Generate Overlapping Cluster Generator (OCG) CommunitiesgetOCG.clusters
Make Node or Edge Graph Featuresgraph.feature
Sample Human Protein Interactomehuman_pp
Convert A Network to an Integer Edgelistinteger.edgelist
Social Network in a Karate Clubkarate
Calculate Node Coordinates for a Spencer Circlelayout.spencer.circle
Co-Appearance Network from Les Miserableslesmiserables
Write a Partition File for Clust&Seelinkcomm2clustnsee
Write an Edge Attribute File for Cytoscapelinkcomm2cytoscape
Calculate Link Community Link DensitiesLinkDensities
Produce a Set of Meta-Communitiesmeta.communities
User-Defined Link CommunitiesnewLinkCommsAt
Extract Node Community Membership by EdgesnumberEdgesIn
Order Link Communities According to the DendrogramorderCommunities
The 'linkcomm' Plotting Functionplot.linkcomm
The 'OCG' Plotting Functionplot.OCG
Plot a Coloured Dendrogram of Link CommunitiesplotLinkCommDend
Plot a Graph Layout of Link CommunitiesplotLinkCommGraph
Plot a Community Membership Matrix for Link CommunitiesplotLinkCommMembers
Plot a Summary of the Link Community Algorithm OutputplotLinkCommSumm
Plot a Summary of the Link CommunitiesplotLinkCommSummComm
Plot a Graph Layout of OCG CommunitiesplotOCGraph
Sample Yeast Protein Interactomepp_rnapol
Print a Summary of a 'linkcomm' Objectprint.linkcomm
Print a Summary of an 'OCG' Objectprint.OCG
Read an OCG Partition File into Rread.OCG
Sample Gene Co-Expression Networkweighted
Extract Community Membership for Nodeswhich.communities