R/Corbi-package.R

#' Corbi - Collection of Rudimentary Bioinformatics Tools
#' 
#' This pakcage provides a bundle of basic and fundamental bioinformatics tools.
#'
#' These bioinformatics tools are developed by \href{http://wulab.aporc.org}{WuLab} at Academy of Mathematics
#' and Systems Science, Chinese Academy of Sciences.
#' 
#' Network querying and alignment:
#' \itemize{
#'   \item \code{\link{net_query}} Network querying method based on conditional random fields
#'   \item \code{\link{net_query_batch}} Batch processing version of \code{\link{net_query}}
#'   \item \code{\link{net_align}} Network alignment method based on conditional random fields
#' }
#' 
#' Subnetwork extraction and search:
#' \itemize{
#'   \item \code{\link{get_subnets}} Enumerate all subnetworks of limited size
#'   \item \code{\link{extend_subnets}} Extend subnetworks from smaller subnetworks
#'   \item \code{\link{best_subnets}} Search best subnetworks that maximize given objective function
#' }
#' 
#' Biomarker identification:
#' \itemize{
#'   \item \code{\link{markrank}} Biomarker identification and prioritization by integrating gene expression with biomolecular network
#' }
#' 
#' @name Corbi-package
#' @aliases Corbi-package Corbi
#' @docType package
#' @keywords package
#' 
#' @references Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. An Efficient
#' Network Querying Method Based on Conditional Random Fields. Bioinformatics,
#' 27(22):3173-3178, 2011.  
#' @references Qiang Huang, Ling-Yun Wu, and Xiang-Sun Zhang. Corbi: A new
#' R package for biological network alignment and querying. BMC Systems Biology,
#' 7(Suppl 2):S6, 2013.
#' 
#' @useDynLib Corbi, .registration = TRUE
#' 
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wulingyun/Corbi documentation built on May 28, 2017, 6:37 a.m.