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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


No version available

Documentation


Maintainers


  • person_outline Heather Turner
  • person_outline Sebastian Kaiser

Publication for biclust

biclust citations

 (12)
library_books

Application of bi clustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

2017
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 […]

library_books

A systematic comparative evaluation of biclustering techniques

2017
BMC Bioinformatics
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), […]

library_books

Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors

2016
BMC Genomics
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 […]

library_books

Evaluation of Plaid Models in Biclustering of Gene Expression Data

2016
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 […]

library_books

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

2015
Beilstein J Nanotechnol
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 […]

library_books

Towards a Hierarchical Strategy to Explore Multi Scale IP/MS Data for Protein Complexes

2015
PLoS One
PMCID: 4598013
PMID: 26448546
DOI: 10.1371/journal.pone.0139704

[…] analyzed again with hc4n., sois are small, which makes it possible to analyze them with other methods for which the full dataset would be too large. we will discuss the soi analysis with the methods biclust [], hiclas [] and apcomplex [] in this publication. biclust [] is used for inducing highly overlapping protein complexes from dense small–scale ip/ms datasets. the method is probabilistic, […]


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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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