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Add ImageJ outputs to the ExperimentHub metadata for the Visium LS data
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 <[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" | ||
| ) | ||
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