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>.

Robust Tests for Differential Dispersion and Differential
Expression in RNA-Sequencing Data
c(person("Jun", "Li", email = "jun.li@nd.edu", role = c("aut", "cre")),
person("Alicia T.", "Lamere", role = c("aut")))
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"DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes"  (Unpublished).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.
Jun Li [aut, cre],
Alicia T. Lamere [aut]

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"DiPhiSeq: Robust comparison of expression levels on RNA-Seq data with large sample sizes"  (Unpublished).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.