% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/HicAggR-package.R
\docType{package}
\name{HicAggR-package}
\alias{HicAggR}
\alias{HicAggR-package}
\title{HicAggR}
\description{
HicAggR is a package that allows to integrate 1D genomics data with
3D genomics data.
This package provides a set of functions useful in the analysis of 3D
genomic interactions. It includes the import of standard HiC data
formats into R and HiC normalisation procedures. The main objective of
this package is to facilitate the visualization and quantification of the
analysis of HiC contacts through aggregation.
The package also provides options to import externally normalized HiC data
to perform an in-depth analysis by investigating genome wide interactions
between features of interest.
The package can use 1D genomics data (such as annotation data or peaks
of features of interest in a GRanges object) to form potential couples
between features of interest under user specified constraints (TADs
coordinates or fixed minimum/max distance). Using these formed couples
it can extract HiC contact data for these specific couples. The submatrices
extracted as such can then be aggregated to summarize genome-wide
interactions, to perform per submatrix operation or compare between
conditions.
It also allows to identify couples with significantly signal-enriched
pixels at specific positions (such as the central pixel) relative to
background less plausible couples.
}
\seealso{
Useful links:
\itemize{
  \item \url{https://cuvierlab.github.io/HicAggR/}
  \item \url{https://github.com/CuvierLab/HicAggR}
  \item Report bugs at \url{https://github.com/CuvierLab/HicAggR/issues}
}

}
\author{
Nicolas Chanard

David Depierre

Robel A Tesfaye

Naomi Schickele

Refka Askri

Pascal Martin

Stéphane Schaack

Olivier Cuvier
}
\keyword{internal}
