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.ac.cn}{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
#' }
#' 
#' Differential expression analysis:
#' \itemize{
#'   \item \code{\link{netDEG}} Sample specific differential expression analysis
#' }
#' 
#' Data normalization:
#' \itemize{
#'   \item \code{\link{URG_getFactor}} Gene expression data normalization by the uniform ratio graph method
#' }
#' 
#' @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.
#' @references Duanchen Sun, Xianwen Ren, Eszter Ari, Tamas Korcsmaros, 
#' Peter Csermely, and Ling-Yun Wu. Discovering cooperative biomarkers for 
#' heterogeneous complex disease diagnoses. Briefings in Bioinformatics, 
#' 20(1), 89–101, 2019.
#' @references Xinhan Ye, Ling-Yun Wu. URG: a new normalization method for 
#' gene expression data based on graph model. Manuscript.
#' 
#' @useDynLib Corbi, .registration = TRUE
#' 
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Corbi documentation built on May 3, 2022, 3:01 a.m.