polyester: Simulate RNA-seq reads

#' Polyester: simulating RNA-seq reads including differential expression
#'
#' Polyester is an R package designed to simulate an RNA sequencing experiment.
#'   Given a set of annotated transcripts, polyester will simulate the steps of
#'   an RNA-seq experiment (fragmentation, reverse-complementing, and 
#'   sequencing) and produce files containing simulated RNA-seq reads. Simulated
#'   reads can be analyzed using any of several downstream analysis tools.
#'
#' A single function call produces RNA-seq reads in FASTA format from a 
#'   case/control experiment including biological replicates. Differential
#'   expression between cases and controls can be set by the user, facilitating
#'   comparisons of statistical differential expression methods for RNA-seq 
#'   data. See detailed documentation for \code{\link{simulate_experiment}} and 
#'   \code{\link{simulate_experiment_countmat}}. 
#' 
#' See the vignette by typing \code{browseVignettes("polyester")} in 
#'   the R prompt.
#' 
#' @references Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, 
#'   Steven L Salzberg, Jeffrey T Leek (2014). Flexible isoform-level 
#'   differential expression analysis with Ballgown. BioRxiv preprint: 
#'   \url{http://biorxiv.org/content/early/2014/03/30/003665}. 
#' @import Biostrings
#' @import IRanges
#' @import S4Vectors
#' @import logspline
#' @importFrom stats loess model.matrix predict rbinom rnbinom rnorm runif smooth.spline
#' @importFrom utils data read.table write.table
#' 
#' @docType package
#' @author Alyssa Frazee, Andrew Jaffe, Rory Kirchner, Jeff Leek
#' @name polyester
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