R/diffloop.R

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

#' diffloop: A package for differential DNA loop calling from ChIA-PET data
#'
#' The diffloop package contains a suite of tools and S4 data objects to
#' efficiently facilitate the analysis of ChIA-PET datasets. Key features
#' include differential loop calling, visualization of looping in regions,
#' quality-control metrics, and principal component analysis across 
#' experiments. 
#' 
#' @section diffloop classes:
#' Three classes mostly comprise the methodology in \code{diffloop}. First,
#' \code{loops} is a basic structure that contains one or more ChIA-PET
#' experiments, \code{loopfit} links an \code{edgeR} fit to a \code{loops}
#' and currently has little functionality except for generating another
#' \code{loops} object where per-loop summary statistics are added.
#'   
#' @docType package
#' @name diffloop
#' @import methods
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