R/derfinder-package.R

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

#'Differential expression analysis of RNA-seq data at base-pair resolution
#'
#'Differential expression analysis of per-nucleotide coverage tables.
#'
#'\tabular{ll}{ Package: \tab derfinder\cr Type: \tab Package\cr Version: \tab
#'1.0.2\cr Date: \tab 2013-04-04\cr License: \tab What license is it under?\cr
#'} Creates SQLite database of per-nucleotide coverage files (\code{makeDb}),
#'fits linear model to each nucleotide to determine differential expression
#'(\code{getLimmaInput},\code{getTstats}), fits Hidden Markov Model using
#'moderated t statistics from linear models as state emissions to get a list of
#'differentially expressed regions (\code{getRegions}), connects found regions
#'with known annotation (\code{getAnnotation}, \code{plotRegion},
#'\code{plotExon}, \code{plotGene}).
#'
#'@name derfinder-package
#'@aliases derfinder-package
#'@docType package
#'@author Alyssa Frazee <afrazee@@jhsph.edu>
#'@references Paper coming soon.
#'@keywords package
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