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#' @keywords internal
#' @aliases scoper-package
"_PACKAGE"
# Project documentation and imports
#' The SCOPer package
#'
#' \code{scoper} is a member of the Immcantation framework and provides computational approaches
#' for the identification of B cell clones from adaptive immune receptor repertoire sequencing
#' (AIRR-Seq) datasets. It includes methods for assigning clonal identifiers using
#' sequence identity, hierarchical clustering, and spectral clustering.
#'
#' @section Clonal clustering:
#'
#' \itemize{
#' \item \link{identicalClones}: Clonal assignment using sequence identity partitioning.
#' \item \link{hierarchicalClones}: Hierarchical clustering approach to clonal assignment.
#' \item \link{spectralClones}: Spectral clustering approach to clonal assignment.
#' }
#'
#' @section Visualization:
#' \itemize{
#' \item \link{plotCloneSummary}: Visualize inter- and intra-clone distances.
#' }
#'
#' @name scoper
#' @docType package
#' @references
#' \enumerate{
#' \item Nouri N and Kleinstein SH (2018). A spectral clustering-based method for identifying clones
#' from high-throughput B cell repertoire sequencing data. Bioinformatics, 34(13):i341-i349.
#' \item Nouri N and Kleinstein SH (2019). Somatic hypermutation analysis for improved identification
#' of B cell clonal families from next-generation sequencing data. bioRxiv, 10.1101/788620.
#' \item Gupta NT, et al. (2017). Hierarchical clustering can identify B cell clones with high
#' confidence in Ig repertoire sequencing data. The Journal of Immunology, 198(6):2489-2499.
#' }
#'
#' @import ggplot2
#' @import graphics
#' @import methods
#' @import utils
#' @importFrom alakazam pairwiseDist checkColumns getDNAMatrix getAAMatrix
#' padSeqEnds progressBar groupGenes baseTheme translateDNA
#' getLocus
#' @importFrom data.table as.data.table .I
#' @importFrom doParallel registerDoParallel
#' @importFrom dplyr n %>% do
#' filter select arrange bind_rows
#' group_by ungroup group_indices
#' mutate summarize slice distinct left_join
#' @importFrom foreach foreach %dopar% registerDoSEQ
#' @importFrom rlang sym syms
#' @importFrom Rcpp evalCpp
#' @importFrom scales pretty_breaks
#' @importFrom shazam consensusSequence
#' @importFrom stats density kmeans sd cor
#' as.dist hclust cutree setNames
#' @importFrom stringi stri_split_fixed stri_length stri_count stri_join
#' @importFrom tidyr separate
#' @useDynLib scoper, .registration=TRUE
NULL
# Package loading actions
.onAttach <- function(libname, pkgname) {
msg <- citation(pkgname)
msg <-paste(c(format(msg,"citation")),collapse="\n\n")
packageStartupMessage(msg)
}
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