From 3b6fbc587b5019a1a703d7cb0b5aed429ee373c0 Mon Sep 17 00:00:00 2001 From: Nick-Eagles Date: Tue, 11 Jun 2024 10:10:03 -0400 Subject: [PATCH] Add metadata and a script to generate it for the Visium LS data --- inst/extdata/metadata_Visium_LS.csv | 3 + inst/scripts/make-metadata_Visium_LS.R | 184 +++++++++++++++++++++++++ 2 files changed, 187 insertions(+) create mode 100644 inst/extdata/metadata_Visium_LS.csv create mode 100644 inst/scripts/make-metadata_Visium_LS.R diff --git a/inst/extdata/metadata_Visium_LS.csv b/inst/extdata/metadata_Visium_LS.csv new file mode 100644 index 00000000..b8a150ea --- /dev/null +++ b/inst/extdata/metadata_Visium_LS.csv @@ -0,0 +1,3 @@ +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 diff --git a/inst/scripts/make-metadata_Visium_LS.R b/inst/scripts/make-metadata_Visium_LS.R new file mode 100644 index 00000000..29a06420 --- /dev/null +++ b/inst/scripts/make-metadata_Visium_LS.R @@ -0,0 +1,184 @@ +library(here) +library(sessioninfo) +library(tidyverse) + +outdir <- "spatialLIBD_files" +pkgname <- "spatialLIBD" + +meta = tibble( + Title = c("Visium_LS_spe", "Visium_LS_spaceranger"), + 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." + ), + BiocVersion = "3.19", + Genome = "GRCh38", + SourceType = c("GTF", "Zip"), + SourceUrl = "https://bioconductor.org/packages/spatialLIBD", + SourceVersion = "June 11 2024", + Species = "Homo sapiens", + TaxonomyId = 9606, + Coordinate_1_based = TRUE, + DataProvider = "LIBD", + Maintainer = "Leonardo Collado-Torres ", + RDataClass = c("SpatialExperiment", "list"), + DispatchClass = c("Rds", "Zip"), + RDataPath = file.path( + pkgname, + outdir, + c("Visium_LS_spe.rds", "Visium_LS_spaceranger.zip") + ), + Tags = "VisiumLS_Visium_stitched_spatialLIBD" +) + +write_csv(meta, here("inst", "extdata", "metadata_Visium_LS.csv")) + +## Check interactively +if (FALSE) { + AnnotationHubData::makeAnnotationHubMetadata( + here(), fileName = "metadata_Visium_LS.csv" + ) +} + +## Reproducibility information +print("Reproducibility information:") +Sys.time() +proc.time() +options(width = 120) +session_info() + +# ─ 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