Imports: ape, Rdpack, Ternary (>= 1.0), TreeTools (>= 1.3.1.9003),

Imports: ape, Rdpack, Ternary (>= 1.0), TreeTools (>= 1.4.0),

of cladograms, calculating the symmetric quartet distance of Bandelt & Dress
(1986), Reconstructing the shape of a tree from observed dissimilarity data,
person("Christian N. S.", "Pedersen", email="cstorm@birc.au.dk",
Imports: ape, Rdpack (>= 0.7), Ternary (>= 1.0), viridisLite,

Description: This package is used to apply the QL, QLShrink and
QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012)
to quasi-Poisson or quasi-negative binomial models for
identifying differentially expressed genes in RNA-seq data.

Title: Analyzing RNA Sequencing Count Tables Using Quasi-Likelihood
person("Long", "Qu", role=c("aut", "cre","ctb"), email="rtistician@gmail.com"),
person("", "R Core Team", role="aut", comment="The author of stats::glm.fit, which was modified slightly leading to glm.fit3 in this package.")
Imports: edgeR, mgcv, pracma, uniqueAtomMat (>= 0.1-1), utils,
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with 'QL', 'QLShrink' and 'QLSpline' methods described by Lund, Nettleton, McCarthy, and Smyth (2012) <DOI:10.1515/1544-6115.1826>. Report bias-reduced estimates of log fold changes.

person("Steve", "Lund", role=c("aut", "cre"), email="lundsp@gmail.com"),
Imports: edgeR, mgcv, pracma, utils, grDevices, graphics

Title: Analyzing RNA sequence count tables using quasi-likelihood
Author: Steve Lund <lundsp@gmail.com> and Long Qu <long.qu@wright.edu>
Description: This package is used to apply the QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012) to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data.

Title: Analyzing RNA Sequence Count Tables Using Quasi-likelihood
Description: Identify differentially expressed genes in RNA-seq count data using quasi-Poisson or quasi-negative binomial models with QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012).