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Add ImageJ outputs to the ExperimentHub metadata for the Visium LS data
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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 <[email protected]>,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 <[email protected]>,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 <[email protected]>,list,Zip,spatialLIBD/spatialLIBD_files/Visium_LS_imagej_out.zip,VisiumLS_Visium_stitched_spatialLIBD |
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@@ -6,27 +6,31 @@ outdir <- "spatialLIBD_files" | |
pkgname <- "spatialLIBD" | ||
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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", | ||
TaxonomyId = 9606, | ||
Coordinate_1_based = TRUE, | ||
DataProvider = "LIBD", | ||
Maintainer = "Leonardo Collado-Torres <[email protected]>", | ||
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" | ||
) | ||
|