% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/derfinder-package.R
\docType{package}
\name{derfinder-package}
\alias{derfinder-package}
\title{Annotation-agnostic differential expression analysis of RNA-seq data at 
base-pair resolution via the DER Finder approach.}
\description{
This package contains two different implementations of the DER Finder 
approach. The first one is the single base-level F-statistics implementation 
and the second one is via identifying expressed regions.
}
\details{
The single base-level F-statistics analysis pipeline involves loading the 
sample BAM files using \link{rawFiles} and \link{loadCoverage}, 
pre-processing the data by using \link{preprocessCoverage}, calculating the 
F-statistics (while adjusting for some confounders) using \link{makeModels} 
and \link{calculateStats}, calculating the p-values and finding the regions 
of interest using \link{calculatePvalues}, and finally annotating them using 
\link[bumphunter]{matchGenes} from the bumphunter package.

The DER Finder at the expressed regions-level is done with
the \link{regionMatrix} or \link{railMatrix} functions depending on the
input data.

Details about both approaches are further described in the vignettes.

The DER Finder approach can also be used to identify differentially bounded
ChIP-seq regions (peaks). In particular, \link{analyzeChr} has parameters 
that allow smoothing of the F-statistics which can be useful for anlayzing
ChIP-seq data. This use case is further explained in the users guide 
vignette.
}
\references{
Collado-Torres L, Frazee AC, Love MI, Irizarry RA, Jaffe AE and Leek JT 
(2015). derfinder: Software for annotation-agnostic RNA-seq differential 
expression analysis. bioRxiv (2015). doi:10.1101/015370

Frazee, A. C., Sabunciyan, S., Hansen, K. D., Irizarry, R. A. & 
Leek, J. T. Differential expression analysis of RNA-seq data at single-base 
resolution. Biostatistics (2014). doi:10.1093/biostatistics/kxt053

Rafael A. Irizarry, Martin Aryee, Hector Corrada Bravo, Kasper D. Hansen and 
Harris A. Jaffee. bumphunter: Bump Hunter. R package version 1.1.10.
}
\author{
Leonardo Collado-Torres <lcollado@jhu.edu>
}
\keyword{package}
