Description: Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms or epistatic interactions, especially high-order epistatic interactions, are important topics in bioinformatics because of their significant mathematical and computational challenges. We present CINOEDV (Co-Information based N-Order Epistasis Detector and Visualizer) for detecting, visualizing, and analyzing high-order epistatic interactions by introducing virtual vertices into the construction of a hypergraph. CINOEDV was developed as an alternative to existing software to build a global picture of epistatic interactions and unexpected high-order epistatic interactions, which might provide useful clues for understanding the underlying genetic architecture of complex diseases.

Title: Calculate Chromosomal Instability Metrics
Author: Vishal H. Oza, Roshan Darji, Brittany N. Lasseigne
Maintainer: Vishal H. Oza <vishoza@uab.edu>
Description: Implement various chromosomal instability metrics. 'CINmetrics' (Chromosomal INstability metrics) provides functions to
calculate various chromosomal instability metrics on masked Copy Number Variation(CNV) data at individual sample level. The
chromosomal instability metrics have been implemented as described in the following studies:
Baumbusch LO et al. 2013 <doi:10.1371/journal.pone.0054356>,
Davidson JM et al. 2014 <doi:10.1371/journal.pone.0079079>,

Title: Computationally-Efficient Confidence Intervals for Mean Shift
person("Jerzy", "Wieczorek", email = "jawieczo@colby.edu", role = c("cre", "aut"),
person("Mara", "Tableman", role = "ctb"))
Description: Implements computationally-efficient construction of
confidence intervals from permutation or randomization tests
based on Nguyen (2009) <https://archives.pdx.edu/ds/psu/37406>.
Jerzy Wieczorek [cre, aut] (<https://orcid.org/0000-0002-2859-6534>),

Title: Covariates, Interaction, and Selection for DGLM
Authors@R: c(person("Ann Stapleton", role = "aut",
person("Yishi Wang", role = c("aut","cre"),email = "wangy@uncw.edu"),
person("Kaitlyn Hohmeier", role = "aut"),
Description: An implementation of double generalized linear model (DGLM) building with variable selection procedures and handling of interaction terms and other complex situations. We also provide a method of handling convergence issues within the dglm() function. The package offers a simulation function for generating simulated data for testing purposes and utilizes the forward stepwise variable selection procedure in model-building. It also provides a new custom bootstrap function for mean and standard deviation estimation and functions for building crossplots and squareplots from a data set.
Imports: ggplot2, dglm, RColorBrewer, dplyr
Packaged: 2022-01-14 16:56:36 UTC; yishiwang