biclust specifications

Information


Unique identifier OMICS_16816
Name biclust
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Requirements
methods, R(≥2.10), flexclust, grid, lattice, ggplot2, MASS, isa2, tidyr, colorspace, additivityTests
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Heather Turner <>
  • person_outline Sebastian Kaiser <>

Publication for biclust

biclust in publications

 (12)
PMCID: 5683856
PMID: 29159232
DOI: 10.1016/j.dib.2017.10.060

[…] from further analysis. all studies were merged together using the gene symbol. the resulting dataset consisted of 8752 gene symbols., the bi-clustering data analysis was conducted in r using the biclust package . the bimax method was selected for this analysis. bimax uses a simple data model that assumes two possible states for each expression level, no change and change with respect […]

PMCID: 5259837
PMID: 28114903
DOI: 10.1186/s12859-017-1487-1

[…] formulation that covers probabilistic/fuzzy, exclusive hard and non-exclusive hard clusterings., most of the codes we used in our experiments were available as packages for the r language, such as: biclust [], fabia [] and isa2 []. we also used the scikit-learn [] and biclustlib (developed by the authors of this paper and available in https://bitbucket.org/padilha/biclustlib), […]

PMCID: 5073849
PMID: 27769165
DOI: 10.1186/s12864-016-3134-z

[…] results for individual datasets and discover the genes that consistently co-express in all three datasets. smart and bi-copam algorithms were implemented in matlab, and bimax from the biclust package in r. we took the median of the replicates in each population. therefore, we have 11 population points for adult blood (namely d0, sem-f d4, sem-i d4, sem-f d7-, sem-f d7+, sem-f d7 […]

PMCID: 4804094
PMID: 27051553
DOI: 10.1155/2016/3059767

[…] were sampled through biopsy. numbers of assayed genes were 2453., in this section, we implemented the plaid algorithms on two simulate datasets and then evaluated them. in this study two r packages, biclust and bioconductor, were used. as shown in , this algorithm was applied to matrix with size of 50 × 20. when there was no noise, the algorithm was capable of discovering biclusters […]

PMCID: 4734442
PMID: 26885455
DOI: 10.3762/bjnano.6.252

[…] to minimize the cross-platform differences. however, platform differences may exist through compression of the fold-change values []., the biclustering data analysis was conducted in r using the biclust [] package. the repeated bimax [] method was selected for this analysis. bimax uses a simple data model that assumes two possible states for each expression level, no change and change […]


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biclust institution(s)
Department of Mathematical Sciences, University of Exeter, Laver Building, Exeter, UK
biclust funding source(s)
Supported by the Wellcome Trust between Imperial College and the Relman Laboratory, Stanford University.

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