Title: Linear Model Bias Correction for RNA-Seq Data
Description: This is the package for implementing the method in "Bias
Correction in RNA-Seq Short-read Counts using Penalized
Regression." It first using a penalized regression to determine
an appropriate surrounding sequence, then refits the model

Description: This is the package for implementing the method in "Bias Correction in RNA-Seq Short-read Counts using Penalized Regression." It first using a penalized regression to determine an appropriate surrounding sequence, then refits the model using the dinucleotide expansion.

Authors@R: person("Megan", "Heyman", email="heyman@rose-hulman.edu", role=c("aut","cre"))
Description: Various efficient and robust bootstrap methods are implemented for
linear models with least squares estimation.  Functions within this package
allow users to create bootstrap sampling distributions for model parameters,
test hypotheses about parameters, and visualize the bootstrap sampling or null
distributions.  Methods implemented for linear models include the wild bootstrap by
Wu (1986) <doi:10.1214/aos/1176350142>, the residual and paired bootstraps by
Efron (1979, ISBN:978-1-4612-4380-9), the delete-1 jackknife by
Quenouille (1956) <doi:10.2307/2332914>, and the Bayesian bootstrap by

A fast dimensionality reduction method scaleable to large numbers of samples.
Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS,
but rather than calculating a complete distance matrix between all pairs of samples,
only the distances between a set of landmarks and the samples are calculated.
Imports: assertthat, dynutils (>= 1.0.3), irlba, Matrix

Title: Linear mixed-effects models using S4 classes
Author: Douglas Bates <bates@stat.wisc.edu>, and
Description: Fit linear and generalized linear mixed-effects models.

Depends: methods, R(>= 1.8.0), R(<= 1.8.1), lattice

Packaged: Thu Mar 11 11:15:47 2004; bates

Author: Douglas Bates <bates@stat.wisc.edu> and
Depends: methods, R(>= 1.9.0), lattice, stats4, Matrix(>= 0.8-6)
Packaged: Tue Jun  1 15:53:30 2004; bates