Add LFF_ERC_spatial data to fetch_data()

R/fetch_data.R

@@ -103,7 +103,15 @@ fetch_data <-
             "Visium_SPG_AD_Visium_wholegenome_modeling_results",
             "visiumStitched_brain_spe",
             "visiumStitched_brain_spaceranger",
-            "visiumStitched_brain_Fiji_out"
+            "visiumStitched_brain_Fiji_out",
+            "LFF_spatial_ERC_SRT",
+            "LFF_spatial_ERC_SRT_pseudobulk",
+            "LFF_spatial_ERC_SRT_modeling_results",
+            "LFF_spatial_ERC_snRNAseq",
+            "LFF_spatial_ERC_snRNAseq_pseudobulk_broad",
+            "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster",
+            "LFF_spatial_ERC_snRNAseq_modeling_results_broad",
+            "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster"
         ),
         destdir = tempdir(),
         eh = ExperimentHub::ExperimentHub(),
@@ -286,6 +294,70 @@ fetch_data <-
             file_name <- "visiumStitched_brain_fiji_out.zip"
             url <-
                 "https://www.dropbox.com/scl/fi/bevo52e96f2kdwllf8dkk/visiumStitched_brain_fiji_out.zip?rlkey=ptwal8f5zxakzejwd0oqw0lhj&dl=1"
+        } else if (type == "LFF_spatial_ERC_SRT") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "spe_ERC_annotated.zip"
+          url <-
+            "https://www.dropbox.com/scl/fi/jrfc2tllppk52yqm1zyb3/spe_ERC_annotated.zip?rlkey=shi4pn3acf916dtscin32zjsn&dl=1"
+        } else if (type == "LFF_spatial_ERC_SRT_pseudobulk") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "spe_pseudobulk-SpD.rds"
+          url <-
+            "https://www.dropbox.com/scl/fi/2cl002smtcl37vaawodil/spe_pseudobulk-SpD.rds?rlkey=6igag1uggpg7h70ruucbl7leb&dl=1"
+        }else if (type == "LFF_spatial_ERC_SRT_modeling_results") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "modeling_results-SpD.rds"
+          url <-
+            "https://www.dropbox.com/scl/fi/4emtnag2x2usb8t4njvb9/modeling_results-SpD.rds?rlkey=d2qr82rz6uargnthkkahrs7e1&dl=1"
+        } else if (type == "LFF_spatial_ERC_snRNAseq") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "sce_ERC_subcluster.zip"
+          url <-
+            "https://www.dropbox.com/scl/fi/plekynuzpb22ii08pcn4j/sce_ERC_subcluster.zip?rlkey=bsgqc5dx4o0memidhs943qdhx&dl=1"
+        } else if (type == "LFF_spatial_ERC_snRNAseq_pseudobulk_broad") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "sce_subcluster_pseudobulk-cell_type_broad.rds"
+          url <-
+            "https://www.dropbox.com/scl/fi/supihrwunx99ldzztzecm/sce_subcluster_pseudobulk-cell_type_broad.rds?rlkey=uy7zmoifjhetfglrav4i2j0ns&dl=1"
+        } else if (type == "LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "sce_subcluster_pseudobulk-cell_type_anno.rds"
+          url <-
+            "https://www.dropbox.com/scl/fi/c1n4i90k5pny7lij3gvxv/sce_subcluster_pseudobulk-cell_type_anno.rds?rlkey=v3kyay0p2i3h24u7c8fx2dn7u&dl=1"
+        } else if (type == "LFF_spatial_ERC_snRNAseq_modeling_results_broad") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "sce_subcluster_pseudobulk-cell_type_broad.rds"
+          url <-
+            "https://www.dropbox.com/scl/fi/eu9z1qp3gx5verdadwpyu/sce_subcluster_modeling_results-cell_type_broad.rds?rlkey=lwd66c7x5vdqeky431unanp45&dl=1"
+        } else if (type == "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster") {
+          tag <- "LFF_spatial_ERC"
+          hub_title <- type
+
+          ## While EH is not set-up
+          file_name <- "sce_subcluster_pseudobulk-cell_type_anno.rds"
+          url <-
+            "https://www.dropbox.com/scl/fi/y42pv7k02luvznwqii2rm/sce_subcluster_modeling_results-cell_type_anno.rds?rlkey=17c0ybowjpejdxc71tuxlcfna&dl=1"
         }
 
         file_path <- file.path(destdir, file_name)

inst/extdata/metadata_LFF_spatial_ERC.csv

@@ -0,0 +1,9 @@
+Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags
+LFF_spatial_ERC_SRT,SpatialExperiment object at the spot-level for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 31) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,SpatialExperiment,FilePath,spatialLIBD/spatialLIBD_files/spe_ERC_annotated.zip,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_SRT_pseudobulk,Pseudo-bulked SingleCellExperiment object (SpatialExperiment object without spatial data) at the Sp09D spatial domain resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 31) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/spe_pseudobulk-SpD.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_SRT_modeling_results,List of modeling results at the Sp09D spatial domain resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (n = 30) from the Visium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,list,Rds,spatialLIBD/spatialLIBD_files/modeling_results-SpD.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_snRNAseq,"SingleCellExperiment object for the LFF_spatial_ERC human brain (ERC) single nucleus transcriptomics data (snRNA-seq, n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,SingleCellExperiment,FilePath,spatialLIBD/spatialLIBD_files/sce_ERC_subcluster.zip,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_snRNAseq_pseudobulk_broad,"Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (n = 31) at 9 broad cell type resolution, from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_DGE-cell_type_broad.RDS,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster,"Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (n = 31) at 38 subcluster resolution, from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.",3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_DGE-cell_type_anno.RDS,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_snRNAseq_modeling_results_broad,List of modeling results at the 9 broad cell type resolution for the LFF_spatial_ERC human brain (ERC) for snRNA-seq (n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,list,Rds,spatialLIBD/spatialLIBD_files/sce_subcluster_pseudobulk-cell_type_broad.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD
+LFF_spatial_ERC_snRNAseq_modeling_results_subcluster,List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) for snRNA-seq (n = 31) from the Chromium platform from 10x Genomics generated by the Lieber Institute for Brain Development (LIBD) and available through the spatialLIBD Bioconductor package.,3.17,GRCh38,GTF,https://bioconductor.org/packages/spatialLIBD,Nov 20 2025,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres <lcolladotor@gmail.com>,list,Rds,spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD