@@ -4,6 +4,8 @@

 #' 

 #' @param sequences Character vector of 30bp sequences needed for DeepSpCas9

 #'     scoring, see details below.

+#' @param fork Set to \code{TRUE} to preserve changes to the R

+#'     configuration within the session.

 #' 

 #' @details The input sequences for DeepSpCas9 scoring require 4 nucleotides

 #'     upstream of the protospacer sequence, the protospacer sequence

@@ -15,7 +17,7 @@

 #'     takes on a value between 0 and 1. A higher score indicates higher

 #'     knockout efficiency.

 #' 

-#' @reference

+#' @references

 #' Kim HK, Kim Y, Lee S, et al. SpCas9 activity prediction by DeepSpCas9, 

 #'     a deep learning–base model with high generalization performance.

 #'     Science advances. 2019 Nov 6;5(11):eaax9249.

@@ -31,7 +33,6 @@

 #' input  <- paste0(flank5, spacer, pam, flank3) 

 #' results <- getDeepSpCas9Scores(input)

 #' }

-#' 

 #' @export 

 #' @importFrom basilisk basiliskStart basiliskStop basiliskRun

 getDeepSpCas9Scores <- function(sequences,

@@ -9,6 +9,9 @@ getDeepSpCas9Scores(sequences, fork = FALSE)

 \arguments{

 \item{sequences}{Character vector of 30bp sequences needed for DeepSpCas9

 scoring, see details below.}

+

+\item{fork}{Set to \code{TRUE} to preserve changes to the R

+configuration within the session.}

 }

 \value{

 \strong{getDeepSpCas9Scores} returns a data.frame with

@@ -35,7 +38,11 @@ flank3 <- "AAT" #3bp

 input  <- paste0(flank5, spacer, pam, flank3) 

 results <- getDeepSpCas9Scores(input)

 }

-

+}

+\references{

+Kim HK, Kim Y, Lee S, et al. SpCas9 activity prediction by DeepSpCas9, 

+    a deep learning–base model with high generalization performance.

+    Science advances. 2019 Nov 6;5(11):eaax9249.

 }

 \author{

 Jean-Philippe Fortin