Biocheck cleared

DESCRIPTION

@@ -1,23 +1,24 @@
 Package: SpatialDatasets
-Version: 0.99.0
+Version: 0.99.1
 Title: Collection of spatial omics datasets
 Description: This is a collection of publically available spatial omics datasets.
   Where possible we have curated these datasets as either SpatialExperiments, 
   MoleculeExperiments or CytoImageLists and included annotations of the sample
   characteristics. 
 Authors@R: c(person("Farhan", "Ameen", email = "[email protected]",
-    role = c("aut", "cre")),
+    role = c("aut")),
     person("Nick", "Robertson", email = "[email protected]",
     role = c("aut")),
     person("Alex", "Qin", email = "[email protected]",
     role = c("aut")),
-    person("Shila", "Ghazanfar", email = "[email protected]",
+    person("Elijah", "Willie", email = "[email protected]",
     role = c("aut")),
     person("Ellis", "Patrick", email = "[email protected]",
-    role = c("aut")))
+    role = c("aut", "cre")))
 URL: https://github.com/SydneyBioX/SpatialDatasets
 BugReports: https://github.com/SydneyBioX/SpatialDatasets/issues
-License: MIT + file LICENSE
+License: GPL-3
+Encoding: UTF-8
 biocViews:
     ExperimentData, 
     ExperimentHub, 

NAMESPACE

@@ -1,3 +1,4 @@
-importFrom(utils, read.csv)
-importFrom(SpatialExperiment, SpatialExperiment)
-importFrom(ExperimentHub, createHubAccessors)
+# Generated by roxygen2: do not edit by hand
+
+importFrom(ExperimentHub,createHubAccessors)
+importFrom(utils,read.csv)

R/zzz.R

@@ -1,3 +1,5 @@
+#' @importFrom utils read.csv
+#' @importFrom ExperimentHub createHubAccessors
 .onLoad <- function(libname, pkgname) {
   fl <- system.file("extdata", "metadata.csv", package=pkgname)
   titles <- read.csv(fl, stringsAsFactors=FALSE)$Title

inst/extdata/metadata.csv

@@ -1,2 +1,2 @@
 "BiocVersion","Genome","SourceVersion","Coordinate_1_based","DataProvider","Maintainer","DispatchClass","Title","Description","SourceUrl","Species","TaxonomyId","RDataPath","RDataClass","SourceType"
-"3.17",NA,NA,NA,NA,"Ellis Patrick <[email protected]>","Rds","spe_Keren_2018","A study on triple negative breast cancer containing samples measured using MIBI-TOF","https://www.angelolab.com/mibi-data","Homo sapiens","9606","SpatialDatasets/spe_Keren_2018.rds","SpatialExperiment","TIFF"
+"3.18",NA,NA,NA,NA,"Ellis Patrick <[email protected]>","Rds","spe_Keren_2018","A study on triple negative breast cancer containing samples measured using MIBI-TOF","https://www.angelolab.com/mibi-data","Homo sapiens","9606","SpatialDatasets/spe_Keren_2018.rds","SpatialExperiment","TIFF"

inst/scripts/make-metadata.R

@@ -5,7 +5,7 @@
 # metadata for all datasets
 
 df_all <- data.frame(
-  BiocVersion = "3.17", 
+  BiocVersion = "3.18", 
   Genome = NA, 
   SourceVersion = NA, 
   Coordinate_1_based = NA, 

man/SpatialDatasets.Rd

@@ -28,6 +28,9 @@ The \code{SpatialDatasets} package contains the following datasets:
 containing 40 samples measured using MIBI-TOF published by [Keren et al. (2018)](https://doi.org/10.1016/j.cell.2018.08.039). 
 }
 }
+\value{
+The datasets will be a SpatialExperiment or MoleculeExperiment.
+}
 \examples{
 # load using dataset name
 spe <- spe_Keren_2018()

vignettes/SpatialDatasets_overview.Rmd

@@ -58,7 +58,7 @@ remotes::install_github("SydneyBioX/SpatialDatasets", build_vignettes = TRUE)
 The package contains the following datasets:
 
 - `spe_Keren_2018`: A study on triple negative breast cancer 
-containing XXX samples measured using MIBI-TOF published by [Keren et al. (2018)](https://doi.org/10.1016/j.cell.2018.08.039). 
+containing 40 samples measured using MIBI-TOF published by [Keren et al. (2018)](https://doi.org/10.1016/j.cell.2018.08.039). 
 
 # Load data