Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.

Coalescent simulators can rapidly simulate biological sequences
    evolving according to a given model of evolution.
    You can use this package to specify such models, to conduct the simulations
    and to calculate additional statistics from the results (Staab, Metzler,
    2016 <doi:10.1093/bioinformatics/btw098>).
    It relies on existing simulators for doing the simulation, and currently
    supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
    mutation models by combining the simulators with the program 'seq-gen'.
    Coala provides functions for calculating certain summary statistics, which
    can also be applied to actual biological data.
    One possibility to import data is through the 'PopGenome' package
    (<https://github.com/pievos101/PopGenome>).

Flexible framework for coalescent analyses in R. It includes a main function running the  MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.

A covariate-augmented overdispersed Poisson factor model is proposed to jointly perform a high-dimensional Poisson factor analysis and estimate a large coefficient matrix for overdispersed count data.
    More details can be referred to Liu et al. (2024) <doi:10.1093/biomtc/ujae031>.

Functions to analyze coarse data.
    Specifically, it contains functions to (1) fit parametric accelerated
    failure time models to interval-censored survival time data, and (2)
    estimate the case-fatality ratio in scenarios with under-reporting.
    This package's development was motivated by applications to infectious
    disease: in particular, problems with estimating the incubation period and
    the case fatality ratio of a given disease.  Sample data files are included
    in the package. See Reich et al. (2009) <doi:10.1002/sim.3659>, 
    Reich et al. (2012) <doi:10.1111/j.1541-0420.2011.01709.x>, and 
    Lessler et al. (2009) <doi:10.1016/S1473-3099(09)70069-6>.