diff --git a/R/listSims.R b/R/listSims.R index fd19aab2e122981f4837a4ba02611c06f97c68e8..2fc06d168bdd2552b2e0dbead7e40e633be7187e 100644 --- a/R/listSims.R +++ b/R/listSims.R @@ -12,22 +12,27 @@ #' @export listSims <- function(print = TRUE) { - sims <- list(c("Splat", "splat", "", "", + sims <- list(c("Splat", "splat", "10.1186/s13059-017-1305-0", + "Oshlack/splatter", "The Splat simulation generates means from a gamma distribution, adjusts them for BCV and generates counts from a gamma-poisson. Dropout and batch effects can be optionally added."), - c("Splat Single", "splatSingle", "", "", + c("Splat Single", "splatSingle", "10.1186/s13059-017-1305-0", + "Oshlack/splatter", "The Splat simulation with a single population."), - c("Splat Groups", "splatGroups", "", "", + c("Splat Groups", "splatGroups", "10.1186/s13059-017-1305-0", + "Oshlack/splatter", "The Splat simulation with multiple groups. Each group can have it's own differential expression probability and fold change distribution."), - c("Splat Paths", "splatPaths", "", "", + c("Splat Paths", "splatPaths", "10.1186/s13059-017-1305-0", + "Oshlack/splatter", "The Splat simulation with differentiation paths. Each path can have it's own length, skew and probability. Genes can change in non-linear ways."), - c("Simple", "simple", "", "", + c("Simple", "simple", "10.1186/s13059-017-1305-0", + "Oshlack/splatter", "A simple simulation with gamma means and negative binomial counts."), c("Lun", "lun", "10.1186/s13059-016-0947-7", diff --git a/R/splat-simulate.R b/R/splat-simulate.R index 98dd989939ca7aa147716f880fea1c2850dae8b4..5f21bebb46f7d2bd164d89bd3d6bc41b2d662852 100644 --- a/R/splat-simulate.R +++ b/R/splat-simulate.R @@ -91,6 +91,14 @@ #' @return SingleCellExperiment object containing the simulated counts and #' intermediate values. #' +#' @references +#' Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA +#' sequencing data. Genome Biology (2017). +#' +#' Paper: \url{10.1186/s13059-017-1305-0} +#' +#' Code: \url{https://github.com/Oshlack/splatter} +#' #' @seealso #' \code{\link{splatSimLibSizes}}, \code{\link{splatSimGeneMeans}}, #' \code{\link{splatSimBatchEffects}}, \code{\link{splatSimBatchCellMeans}}, diff --git a/inst/CITATION b/inst/CITATION index fbf6993b14214437afa6b9e352dada36ff0c334c..7d56fb8c7b4a92b03a5897f8ab41f4320e2ee728 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,10 +1,10 @@ citEntry( entry = "article", author = "Luke Zappia and Belinda Phipson and Alicia Oshlack", - title = "Splatter: Simulation Of Single-Cell RNA Sequencing Data", - journal = "bioRxiv", + title = "Splatter: simulation of single-cell RNA sequencing data", + journal = "Genome Biology", year = "2017", - url = "http://dx.doi.org/10.1101/133173", - doi = "10.1101/133173", - textVersion = "Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA Sequencing Data. bioRxiv. 2017; doi:10.1101/133173" + url = "http://dx.doi.org/10.1186/s13059-017-1305-0", + doi = "10.1186/s13059-017-1305-0", + textVersion = "Zappia L, Phipson B, Oshlack A. Splatter: Simulation of single-cell RNA sequencing data. Genome Biology. 2017; doi:10.1186/s13059-017-1305-0" ) diff --git a/man/splatSimulate.Rd b/man/splatSimulate.Rd index 1b06a3f563ffccf97a3cf3f193bb78cb08b66826..bf30985a5e88b46e7f516b93e3884463aaf06cc7 100644 --- a/man/splatSimulate.Rd +++ b/man/splatSimulate.Rd @@ -130,6 +130,14 @@ sim <- splatSimulate(method = "groups") sim <- splatSimulate(method = "paths") } } +\references{ +Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA +sequencing data. Genome Biology (2017). + +Paper: \url{10.1186/s13059-017-1305-0} + +Code: \url{https://github.com/Oshlack/splatter} +} \seealso{ \code{\link{splatSimLibSizes}}, \code{\link{splatSimGeneMeans}}, \code{\link{splatSimBatchEffects}}, \code{\link{splatSimBatchCellMeans}},