CFinder protocols

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CFinder specifications


Unique identifier OMICS_11243
Name CFinder
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.0.6
Stability Stable
Maintained Yes


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Publication for CFinder

CFinder in pipeline

PMCID: 3471511
PMID: 23087704
DOI: 10.3389/fgene.2012.00208

[…] to randomly generated network null models of same graph constraints. this was achieved via a network analysis utility graphcrunch2 (milenkovic et al., ). the k-clique community finding tool “cfinder” was used to grab the community structures (closely interlinked sub-graphs) in the core molecular network (k = 3). this method first locates all cliques of the network and then identifies […]

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CFinder in publications

PMCID: 5895626
PMID: 29643399
DOI: 10.1038/s41598-018-24224-2

[…] and have intensities above the threshold. hence, the communities are dependent on the number of nodes k in a clique and the intensity threshold i., the cpm algorithm is implemented in the program cfinder. using the edge list of the gaussian graphical model estimated on the scl-90-r data, we determined, for each k, the optimal intensity threshold i to obtain the richest community structure. […]

PMCID: 5845728
PMID: 29559981
DOI: 10.3389/fimmu.2018.00449

[…] corresponding ppi network was constructed. a score of ≥0.7 for each ppi pair was selected to design the ppi network., to detect high-flow areas (highly connected regions) of the network, we used the cfinder software tool, based on the clique percolation method (cpm) (). finally, cytoscape software () was used to define the topology of the built networks., to isolate cell-free circulating mirna […]

PMCID: 5913670
PMID: 29474580
DOI: 10.1093/molbev/msy022

[…] from genemania ( only ppis with evidence of biological pathways and physical interactions were used for network construction. the network module was identified using cfinder () requiring clique numbers of >2. the association between network module genes and cell migration function was estimated using cociter with the term “cell migration” with p-value cutoff […]

PMCID: 5836830
PMID: 29504897
DOI: 10.1186/s12859-018-2017-5

[…] as edges. for example, methods such as markov cluster (mcl) [], molecular complex detection (mcode) [], clustering-based on maximal cliques (cmc) [], protein complex prediction (pcp) [], and cfinder [] are mainly based on the topological structures of ppi networks. other methods such as restricted neighborhood search clustering (rnsc) [] and feng et al. [] exploit biological information […]

PMCID: 5814444
PMID: 29449618
DOI: 10.1038/s41598-018-21454-2

[…] two nucleotide (tnms) and three nucleotide (thnms) network motifs were enumerated for each nucleotide co-occurrence network (see legends of fig. ). thnms or clique structures were identified using cfinder and tnms were identified by subtracting nodes participating to form thnms from network adjacency list. after detailing all the motifs based on their positions in codons in different networks […]

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CFinder institution(s)
Department of Biological Physics, Eötvös University, Budapest, Hungary; Biological Physics Research Group of the Hungarian Academy of Sciences, Budapest, Hungary

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