Pvclust: an R package for assessing the uncertainty in hierarchical clustering
Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic...
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| Veröffentlicht in: | Bioinformatics 2006-06, Vol.22 (12), p.1540-1542 |
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| creator | Suzuki, Ryota Shimodaira, Hidetoshi |
| description | Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option. Availability: The program is freely distributed under GNU General Public License (GPL) and can directly be installed from CRAN (), the official R package archive. The instruction and program source code are available at Contact:ryota.suzuki@is.titech.ac.jp |
| doi_str_mv | 10.1093/bioinformatics/btl117 |
| format | Article |
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The instruction and program source code are available at Contact:ryota.suzuki@is.titech.ac.jp</description><subject>Algorithms</subject><subject>Biological and medical sciences</subject><subject>Cluster Analysis</subject><subject>Computational Biology - methods</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>General aspects</subject><subject>Humans</subject><subject>Internet</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. 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Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In addition the computation time can be enormously decreased with parallel computing option. Availability: The program is freely distributed under GNU General Public License (GPL) and can directly be installed from CRAN (), the official R package archive. 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| subjects | Algorithms Biological and medical sciences Cluster Analysis Computational Biology - methods Fundamental and applied biological sciences. Psychology Gene Expression Profiling Gene Expression Regulation, Neoplastic General aspects Humans Internet Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Statistical Oligonucleotide Array Sequence Analysis - methods Probability Programming Languages Software Uncertainty |
| title | Pvclust: an R package for assessing the uncertainty in hierarchical clustering |
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