Pvclust: an R package for assessing the uncertainty in hierarchical clustering Export

@article{citeulike:825687, abstract = {Summary: 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 (http://cran.r-project.org/), the official R package archive. The instruction and program source code are available at http://www.is.titech.ac.jp/\~{}shimo/prog/pvclust Contact: ryota.suzuki@is.titech.ac.jp 10.1093/bioinformatics/btl117}, address = {Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan. ryota.suzuki@is.titech.ac.jp}, author = {Suzuki, Ryota and Shimodaira, Hidetoshi}, citeulike-article-id = {825687}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl117}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/12/1540}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16595560}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16595560}, day = {15}, doi = {10.1093/bioinformatics/btl117}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {clustering, hierarchical, r, software}, month = {June}, number = {12}, pages = {1540--1542}, posted-at = {2006-09-02 11:32:40}, priority = {2}, title = {Pvclust: an R package for assessing the uncertainty in hierarchical clustering}, url = {http://dx.doi.org/10.1093/bioinformatics/btl117}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:825687 L3 - citeulike-article-id:825687 N2 - Summary: 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 (http://cran.r-project.org/), the official R package archive. The instruction and program source code are available at http://www.is.titech.ac.jp/~shimo/prog/pvclust Contact: ryota.suzuki@is.titech.ac.jp 10.1093/bioinformatics/btl117 IS - 12 JF - Bioinformatics SN - 1367-4803 AD - Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan. ryota.suzuki@is.titech.ac.jp EP - 1542 TI - Pvclust: an R package for assessing the uncertainty in hierarchical clustering VL - 22 SP - 1540 KW - clustering KW - hierarchical KW - r KW - software AU - Suzuki, Ryota AU - Shimodaira, Hidetoshi PY - 2006/06/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btl117 ER -