Description: Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA' package). Using the framework of linear model-based differential expression comparisons ('limma' package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.

Title: Robust Tests for Differential Dispersion and Differential
Authors@R: c(person("Jun", "Li", email = "jun.li@nd.edu", role = c("aut", "cre")),
person("Alicia T.", "Lamere", role = c("aut")))
Description: Implements the algorithm described in Jun Li and Alicia T. Lamere,
"DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes"  (Unpublished).
Detects not only genes that show different
average expressions ("differential expression", DE), but also genes that show different
diversities of expressions in different groups ("differentially dispersed", DD). DD genes
can be important clinical markers. 'DiPhiSeq' uses a redescending penalty on the
quasi-likelihood function, and thus has superior robustness against outliers and other noise.

Updates from version 0.1.0: (1) Added the option of using adaptive initial value for phi.
(2) Added a function for estimating the proportion of outliers in the data.
(3) Modified the input parameter names for clarity, and modified the output format for the main function.

Title: Directional Penalties for Optimal Matching in Observational
Description: Improves the balance of optimal matching with near-fine balance by giving penalties on the unbalanced covariates with the unbalanced directions. Many directional penalties can also be viewed as Lagrange multipliers, pushing a matched sample in the direction of satisfying a linear constraint that would not be satisfied without penalization.
Imports: rcbalance, stats, liqueueR, plyr, mvnfast, methods
Note: One minimum cost flow problem may have several or many solutions
that are equivalent in providing the same minimum total or mean
cost. Minor differences between computers or implementations
may have the minor consequence of altering which equivalent