% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/csdR-package.R
\docType{package}
\name{csdR}
\alias{csdR-package}
\alias{csdR}
\title{Perform differential co-expression analysis}
\description{
This package provides functionality
to perform differential co-expression
analysis by the CSD algorithm presented by Voigt et al. 2017.
The main function of the
package is \code{\link{run_csd}} which compares gene expression for two
conditions and returns values for C, S and D for each gene pair.
Also, the underlying
function \code{\link{run_cor_bootstrap}} is provided
for doing correlation analysis
\emph{within} a condition,
but is mostly for experimental and expect use only.

The function \code{\link{partial_argsort}} is
aimed specifically at the task of
selecting the highest values of C, S and D
of the results with minimal computational overhead,
but is written also to be useable for other problems of the same type.

For more details on how to approach, please read the
vignette for the package or the individual manpages for the functions.
}
\references{
Voigt A, Nowick K and Almaas E
'A composite network of conserved and tissue specific
gene interactions reveals possible genetic interactions in glioma'
In: \emph{PLOS Computational Biology} 13(9): e1005739.
(doi: \url{https://doi.org/10.1371/journal.pcbi.1005739})
}
\seealso{
Useful links:
\itemize{
  \item \url{https://almaaslab.github.io/csdR}
  \item \url{https://github.com/AlmaasLab/csdR}
  \item Report bugs at \url{https://github.com/AlmaasLab/csdR/issues}
}

}
\author{
\strong{Maintainer}: Jakob Peder Pettersen \email{jakobpeder.pettersen@gmail.com} (\href{https://orcid.org/0000-0002-3485-1634}{ORCID})

}
\keyword{internal}
