@@ -21,9 +21,8 @@ Authors@R: c(

 Description: This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.

 License: GPL (>= 3)

 Encoding: UTF-8

-LazyDataCompression: bzip2

 Roxygen: list(markdown = TRUE)

-RoxygenNote: 7.3.1

+RoxygenNote: 7.3.2

 biocViews: Software, GeneExpression, Transcriptomics, Spatial, CellBiology

 Depends:

   R (>= 4.4)

@@ -6,4 +6,5 @@

 #' @docType data

 #' @references Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M, Chew J. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature neuroscience. 2021 Mar;24(3):425-36.

 #' @source {SpatialLIBD} R/Bioconductor package.

+#' @usage data(HumanDLPFC)

 "HumanDLPFC"

\ No newline at end of file

@@ -156,6 +156,12 @@ plotSpatial <-

     return(p1)

   }

+requirePkg <- function(pkg) {

+  if (!requireNamespace(pkg, quietly = TRUE)) {

+    stop(sprintf("'%s' needed for this function to work.", pkg), call. = FALSE)

+  }

+}

+

 custom_theme <- function(rl = 1.1) {

   stopifnot(rl > 0)

   rl = ggplot2::rel(rl)

@@ -3,7 +3,7 @@ bibentry(

   title    = "SpaNorm: spatially-aware normalisation for spatial transcriptomics data",

   author   = c(

     person("Agus", "Salim", comment = c(ORCID = "0000-0003-3999-7701")),

-    person("Dharmesh D.", "Bhuva"comment = c(ORCID = "0000-0002-6398-9157")),

+    person("Dharmesh D.", "Bhuva", comment = c(ORCID = "0000-0002-6398-9157")),

     person("Carissa", "Chen"),

     person("Pengyi", "Yang"),

     person("Melissa J", "Davis"),

@@ -11,7 +11,7 @@ A SpatialExperiment containing region annotations in the \code{colData} column '

 {SpatialLIBD} R/Bioconductor package.

 }

 \usage{

-HumanDLPFC

+data(HumanDLPFC)

 }

 \description{

 Human DLPFC sample profiled using the 10x Visium platform. Lowly expressed genes were filtered out using the \code{filterGenes} function to retain genes expressed in at least 10\% of samples. This version was obtained from the SpatialLIBD R/Bioconductor package.