Clust protocols

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Popular tool citations

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Associated diseases

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Clust specifications

Information


Unique identifier OMICS_24103
Name Clust
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.4.0
Stability Stable
Requirements
numpy, scipy, matplotlib, sklearn, sompy, joblib, portalocker
Maintained Yes

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Maintainer


  • person_outline Steven Kelly <>

Publication for Clust

Clust in pipelines

 (6)
2016
PMCID: 4886093
PMID: 27294188
DOI: 10.1155/2016/1970904

[…] can offer mechanistic hypotheses of disease because they are highly interconnected molecular complexes or signaling pathways []. in this study, clusters were found with cytoscape plugin called clust&see dedicated to the identification, visualization, and analysis of clusters extracted from ppi network []., the network consists of 74 nodes connected via 453 edges. kdm6a has seven direct […]

2016
PMCID: 5068391
PMID: 27761315
DOI: 10.7717/peerj.2498

[…] protein sequences were aligned with hmmalign (hmmer3 ()) and clustered by complete linkage clustering (mcclust (), fungenepipeline). rarefaction (fungenepipeline ()) was based on data from the clust file at 0.03 distance. conservation analysis of the msma and msme predicted protein sequences was performed on alignments generated by hmmalign (hmmer3) and analyzed by jalview (). alpha […]

2015
PMCID: 4405270
PMID: 25898350
DOI: 10.1371/journal.pntd.0003680

[…] and a computational cluster at the novosibirsk state university., the following primers were used for the amplification of genomic regions hosting the mirna genes of the three opisthorchiid species: clust1-for1 (5'-cacagccagtattgatgaac-3'), clust1-for2 (5'-acagccctgcttgggacac-3'), clust1-rev (5'-ccaaagcttggactgtgat-3'), clust2-for (5'-aaagacttgagtagtgagacgct-3'), clust2-rev […]

2014
PMCID: 4022483
PMID: 24830797
DOI: 10.1371/journal.pcbi.1003598

[…] therefore be difficult to distinguish early and delayed transcriptional regulation from mrna abundance data., to classify the profiles we sample the mean of the latent function ( in ) and use puma-clust to cluster the genes. puma-clust has the advantage of taking into account the uncertainty of the latent function when clustering the profiles. this uncertainty is computed from the posterior […]

2014
PMCID: 4122925
PMID: 24923324
DOI: 10.1093/gbe/evu127

[…] euryarchaeota, thaumarchaeota, nanoarchaeota, korarchaeota, and unclassified archaea) was calculated for each fosmid and the resulting data matrix was processed with a quality cluster method (qt_clust) () with mev (multiexperiment viewer; http://www.tm4.org/mev.html, last accessed june 25, 2014) (). this provided a preliminary ascription of fosmids to different taxonomic groups. […]


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Clust in publications

 (135)
PMCID: 5943561
PMID: 29774217
DOI: 10.3389/fvets.2018.00071

[…] become infected; for γ, the 0.10 indicated that per daily timestep, each infected individual had a 10% probability of recovering. these methods are available through r package enss as functions “clust_sim_si” and “clust_sim_sir,” respectively. although we chose to focus our efforts by using unweighted networks and testing only one value for β, we also present analyses that investigate […]

PMCID: 5886413
PMID: 29621264
DOI: 10.1371/journal.pone.0194462

[…] matrix a used in their definitions is the recurrence matrix from which the identity matrix is subtracted (aij = rij−δij where δij is the kronecker delta) []., the clustering coefficient [] is: clust=∑i=1n∑j,k=1nai,jaj,kak,irri(13) where rri=∑j=1nai,j is the local recurrence rate., the transitivity [] is: trans=∑i,j,k=1najkaijaik∑i,j,k=1naijaik(14), the crp toolbox (provided by tocsy: […]

PMCID: 5880028
PMID: 29610768
DOI: 10.1523/ENEURO.0252-17.2018

[…] across variation of three manner of articulation features (i.e., stop, fricative, and nasal)., generalization maps after correction for multiple comparisons using cluster-size thresholding (p-clust < 0.05) during the performance of the attend to vowels task are presented in . the generalization maps revealed successful decoding of place of articulation within regions of the brain’s […]

PMCID: 5835079
PMID: 29535760
DOI: 10.3389/fgene.2018.00045

[…] both potential inhibitors and activators of rna silencing, were selected and tested in the validation dose-response experiments. data were hierarchically clustered using the python library inchlib_clust and visualized with the corresponding javascript library inchlib (skuta et al., ). the clustering was performed with a combination of the ward's linkage algorithm (ward, ) and the classic […]

PMCID: 5872123
PMID: 29438308
DOI: 10.3390/antibiotics7010012

[…] columns report the affiliated genome, clade, gene cluster class (hybrids are indicated by hyphens), gene cluster length (bp), natural product annotation provided by antismash, cluster membership (clust memb), mibig database identification, the portion of genes with similarity to genes within the most similar known cluster from the mibig database (% genes w/similarity). cluster membership […]


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Clust institution(s)
Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK

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