From b5fed63db7e405ad3d75d36ed4d0a0cce42df4b5 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Fri, 13 Oct 2017 16:39:40 +1100
Subject: [PATCH] Update citation
---
R/listSims.R | 15 ++++++++++-----
R/splat-simulate.R | 8 ++++++++
inst/CITATION | 10 +++++-----
man/splatSimulate.Rd | 8 ++++++++
4 files changed, 31 insertions(+), 10 deletions(-)
diff --git a/R/listSims.R b/R/listSims.R
index fd19aab..2fc06d1 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 98dd989..5f21beb 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 fbf6993..7d56fb8 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 1b06a3f..bf30985 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}},
--
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