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hierBipartite  

Bipartite Graph-Based Hierarchical Clustering
View on CRAN: Click here


Download and install hierBipartite package within the R console
Install from CRAN:
install.packages("hierBipartite")

Install from Github:
library("remotes")
install_github("cran/hierBipartite")

Install by package version:
library("remotes")
install_version("hierBipartite", "0.0.2")



Attach the package and use:
library("hierBipartite")
Maintained by
Calvin Chi
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-02-16
Latest Update: 2021-02-16
Description:
Bipartite graph-based hierarchical clustering, developed for pharmacogenomic datasets and datasets sharing the same data structure. The goal is to construct a hierarchical clustering of groups of samples based on association patterns between two sets of variables. In the context of pharmacogenomic datasets, the samples are cell lines, and the two sets of variables are typically expression levels and drug sensitivity values. For this method, sparse canonical correlation analysis from Lee, W., Lee, D., Lee, Y. and Pawitan, Y. (2011) is first applied to extract association patterns for each group of samples. Then, a nuclear norm-based dissimilarity measure is used to construct a dissimilarity matrix between groups based on the extracted associations. Finally, hierarchical clustering is applied.
How to cite:
Calvin Chi (2021). hierBipartite: Bipartite Graph-Based Hierarchical Clustering. R package version 0.0.2, https://cran.r-project.org/web/packages/hierBipartite. Accessed 22 Dec. 2024.
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Complete documentation for hierBipartite
Functions, R codes and Examples using the hierBipartite R package
Some associated functions: constructBipartiteGraph . ctrp2 . getMergeGroupRows . getSignificantMergedGroups . hierBipartite . matrixDissimilarity . newMergedGroup . null_distri . p_value . scale_features . scca . 
Some associated R codes: HierBipartite.R . data.R . scca.R . utils.R .  Full hierBipartite package functions and examples
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