R/RDAVIDWebService-package.R

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

#' An R Package for retrieving data from DAVID into R objects using Web Services
#'
#' Tools for retrieving data from the Database for Annotation, Visualization
#' and Integrated Discovery (DAVID) using Web Services into R objects.
#' This package offers the main functionalities of DAVID website including:
#' \describe{
#' \item{Connectivity:}{upload gene/background list/s, change gene/background 
#'  position, select current specie/s, select annotations, etc. from R.} 
#' \item{Exploration:}{ native R objects of submitted Gene List, Annotation
#' Category Summary, Gene/Term Clusters, Functional Annotation Chart and
#' Functional Annotation Tables. In addition it offers the usual
#' many-genes-to-many-terms visualization and induced Gene Ontology direct
#' acyclic graph GOstats-based conversion method, in order to visualize GO
#' structure.} 
#' }
#'
#' @docType package
#' @name DAVIDWebService-package
#' @aliases DAVIDWebService-package
#' @rdname DAVIDWebService-package
#' @keywords DAVID SEA MEA
#'
#' @author Cristobal Fresno \email{cristobalfresno@@gmail.com} and Elmer A. 
#' Fernandez \email{elmerfer@@gmail.com}
#' @references 
#' \enumerate{
#'  \item The Database for Annotation, Visualization and Integrated Discovery 
#'  (david.abcc.ncifcrf.gov)
#'  \item Xiaoli Jiao, Brad T. Sherman, Da Wei Huang, Robert Stephens, Michael
#'   W. Baseler, H. Clifford Lane, Richard A. Lempicki, DAVID-WS: A Stateful Web
#'   Service to Facilitate Gene/Protein List Analysis Bioinformatics 2012
#'  \url{doi:10.1093/bioinformatics/bts251}
#'  \item Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.;
#'  Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A DAVID
#'  Bioinformatics Resources: expanded annotation database and novel algorithms
#'  to better extract biology from large gene lists. Nucleic Acids Res,
#'  Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc.,
#'  National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175
#'  \item Cristobal Fresno, Elmer A. Fernandez (2013) RDAVIDWebService: a 
#'  versatile R interface to DAVID, Bioinformatics, 29(21), 2810-2811.,
#'  \url{http://bioinformatics.oxfordjournals.org/content/29/21/2810.}
#' }
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