diff --git a/inst/extdata/metadata_Visium_LS.csv b/inst/extdata/metadata_Visium_LS.csv index b8a150ea..5b868cf7 100644 --- a/inst/extdata/metadata_Visium_LS.csv +++ b/inst/extdata/metadata_Visium_LS.csv @@ -1,3 +1,4 @@ Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags Visium_LS_spe,SpatialExperiment object at the spot-level for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.19,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/Visium_LS_spe.rds,VisiumLS_Visium_stitched_spatialLIBD Visium_LS_spaceranger,Spaceranger outputs for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Zip,spatialLIBD/spatialLIBD_files/Visium_LS_spaceranger.zip,VisiumLS_Visium_stitched_spatialLIBD +Visium_LS_ImageJ_out,Stitched PNG image and XML file from aligning lateral septum human brain (LS) spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package.,3.19,GRCh38,Zip,https://bioconductor.org/packages/spatialLIBD,June 11 2024,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Zip,spatialLIBD/spatialLIBD_files/Visium_LS_imagej_out.zip,VisiumLS_Visium_stitched_spatialLIBD diff --git a/inst/scripts/make-metadata_Visium_LS.R b/inst/scripts/make-metadata_Visium_LS.R index 29a06420..8771569e 100644 --- a/inst/scripts/make-metadata_Visium_LS.R +++ b/inst/scripts/make-metadata_Visium_LS.R @@ -6,14 +6,15 @@ outdir <- "spatialLIBD_files" pkgname <- "spatialLIBD" meta = tibble( - Title = c("Visium_LS_spe", "Visium_LS_spaceranger"), + Title = c("Visium_LS_spe", "Visium_LS_spaceranger", "Visium_LS_ImageJ_out"), Description = c( "SpatialExperiment object at the spot-level for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.", - "Spaceranger outputs for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment." + "Spaceranger outputs for the spatially stitched lateral septum human brain (LS) spatial transcriptomics data (n = 3) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package. Can be used with visiumStitched::build_spe() to construct a SpatialExperiment.", + "Stitched PNG image and XML file from aligning lateral septum human brain (LS) spatial transcriptomics data (n = 3) in ImageJ. Data to align was from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and is available through the spatialLIBD Bioconductor package." ), BiocVersion = "3.19", Genome = "GRCh38", - SourceType = c("GTF", "Zip"), + SourceType = c("GTF", "Zip", "Zip"), SourceUrl = "https://bioconductor.org/packages/spatialLIBD", SourceVersion = "June 11 2024", Species = "Homo sapiens", @@ -21,12 +22,15 @@ meta = tibble( Coordinate_1_based = TRUE, DataProvider = "LIBD", Maintainer = "Leonardo Collado-Torres ", - RDataClass = c("SpatialExperiment", "list"), - DispatchClass = c("Rds", "Zip"), + RDataClass = c("SpatialExperiment", "list", "list"), + DispatchClass = c("Rds", "Zip", "Zip"), RDataPath = file.path( pkgname, outdir, - c("Visium_LS_spe.rds", "Visium_LS_spaceranger.zip") + c( + "Visium_LS_spe.rds", "Visium_LS_spaceranger.zip", + "Visium_LS_imagej_out.zip" + ) ), Tags = "VisiumLS_Visium_stitched_spatialLIBD" )