Title: Multivariate Tools for Compositional Data Analysis
Depends: R (>= 1.8.0), MASS, HardyWeinberg, calibrate
Description: Provides functions for multivariate analysis with compositional data. Includes a function for doing compositional canonical correlation analysis. This analysis requires two data matrices of compositions, which can be adequately transformed and used as entries in a specialized program for canonical correlation analysis, that is able to deal with singular covariance matrices. The methodology is described in Graffelman et al. (2017) <doi:10.1101/144584>.

Depends: R (>= 1.8.0), MASS, calibrate, robCompositions
Description: Provides functions for multivariate analysis with compositional data. Includes a function for doing compositional canonical correlation analysis.  This analysis requires two data matrices of compositions, which can be adequately transformed and used as entries in a specialized program for canonical correlation analysis, that is able to deal with singular covariance matrices. The methodology is described in Graffelman et al. (2017) <doi:10.1101/144584>. A function for log-ratio principal component analysis with condition number computations has been added to the package.

Depends: R (>= 1.8.0), MASS, calibrate, HardyWeinberg

Title: An Efficient and Deterministic Method for Identifying
Imports: matrixStats, grid, ggplot2, reshape2, tibble
Authors@R: c(person("Henrik", "Bengtsson", role = c("aut", "cre", "cph"),
person("Hanjun", "Shin", role = c("aut", "ctr", "cph"),
person("Harris", "Lazaris", role = c("ctr", "cph"),
person("Gangqing", "Hu", role = c("ctr", "cph"),
person("Xianghong", "Zhou", role = c("ctr"),
Description: The 'TopDom' method identifies topological domains in genomes from Hi-C sequence data (Shin et al., 2016 <doi:10.1093/nar/gkv1505>).  The authors published an implementation of their method as an R script (two different versions; also available in this package).  This package originates from those original 'TopDom' R scripts and provides help pages adopted from the original 'TopDom' PDF documentation.  It also provides a small number of bug fixes to the original code.
Harris Lazaris [ctr, cph] (PhD Student, NYU),
Gangqing Hu [ctr, cph] (Staff Scientist, NIH),