GeneralizedUmatrix, shiny, shinyjs, shinythemes, plotly,
spdep, pracma, grid, mgcv, fields, png, reshape2, Rtsne,

Description: A clustering approach applicable to every projection method is proposed here. The two-dimensional scatter plot of any projection method can construct a topographic map which displays unapparent data structures by using distance and density information of the data. The generalized U*-matrix renders this visualization in the form of a topographic map, which can be used to automatically define the clusters of high-dimensional data. The whole system is based on Thrun and Ultsch, "Using Projection based Clustering to Find Distance and Density based Clusters in High-Dimensional Data" <DOI:10.1007/s00357-020-09373-2>. Selecting the correct projection method will result in a visualization in which mountains surround each cluster. The number of clusters can be determined by counting valleys on the topographic map. Most projection methods are wrappers for already available methods in R. By contrast, the neighbor retrieval visualizer (NeRV) is based on C++ source code of the 'dredviz' software package, and the Curvilinear Component Analysis (CCA) is translated from 'MATLAB' ('SOM Toolbox' 2.0) to R.

methods, dendextend, umap, uwot, DatabionicSwarm

methods, dendextend, umap, uwot, DatabionicSwarm, parallelDist

Title: Calculates and Analyzes the Proliferative Index
Authors@R: c(person("Brittany", "Lasseigne", role = c("aut", "cre"),
person("Ryne", "Ramaker", role = "aut", email = "ryneramaker@gmail.com"))
Description: Provides functions for calculating and analyzing the proliferative
index (PI) from an RNA-seq dataset. As described in Ramaker & Lasseigne,

Title: Computes confidence intervals for single proportions, for
differences in proportions, for an odds-ratio and for the
Description: Computes confidence intervals for single proportions and
confidence intervals for differences in proportions in a 2x2

Title: Computes confidence intervals for proportions, differences in
proportions, an odds-ratio and the relative risk in a 2x2 table
Description: Computes confidence intervals for single proportions, for
relative risk in a 2x2 table. Functions available for dependent