diff --git a/DESCRIPTION b/DESCRIPTION index 340b56a..95c6ac0 100644 --- a/DESCRIPTION +++ b/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 = "fame2827@uni.sydney.edu.au", - role = c("aut", "cre")), + role = c("aut")), person("Nick", "Robertson", email = "nick.robertson@sydney.edu.au", role = c("aut")), person("Alex", "Qin", email = "alex.qin@sydney.edu.au", role = c("aut")), - person("Shila", "Ghazanfar", email = "shila.ghazanfar@sydney.edu.au", + person("Elijah", "Willie", email = "shila.ghazanfar@sydney.edu.au", role = c("aut")), person("Ellis", "Patrick", email = "ellis.patrick@sydney.edu.au", - 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, diff --git a/NAMESPACE b/NAMESPACE index c87f2e2..86ea7e1 100644 --- a/NAMESPACE +++ b/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) diff --git a/R/zzz.R b/R/zzz.R index aaa1847..2955c27 100644 --- a/R/zzz.R +++ b/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 diff --git a/inst/extdata/metadata.csv b/inst/extdata/metadata.csv index bd80569..2940419 100644 --- a/inst/extdata/metadata.csv +++ b/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 ","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 ","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" diff --git a/inst/scripts/make-metadata.R b/inst/scripts/make-metadata.R index 42fc359..2cbe70d 100644 --- a/inst/scripts/make-metadata.R +++ b/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, diff --git a/man/SpatialDatasets.Rd b/man/SpatialDatasets.Rd index 988814f..76afbb8 100644 --- a/man/SpatialDatasets.Rd +++ b/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() diff --git a/vignettes/SpatialDatasets_overview.Rmd b/vignettes/SpatialDatasets_overview.Rmd index 6dd3788..514ccb3 100644 --- a/vignettes/SpatialDatasets_overview.Rmd +++ b/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