From cfb0939738f7554b70b7a1e379446c62a46d8143 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Fri, 21 Nov 2025 15:05:49 +0000 Subject: [PATCH 01/10] Add metadata file for spatial ERC --- inst/extdata/metadata_LFF_spatial_ERC.csv | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 inst/extdata/metadata_LFF_spatial_ERC.csv diff --git a/inst/extdata/metadata_LFF_spatial_ERC.csv b/inst/extdata/metadata_LFF_spatial_ERC.csv new file mode 100644 index 00000000..eb8830d7 --- /dev/null +++ b/inst/extdata/metadata_LFF_spatial_ERC.csv @@ -0,0 +1,7 @@ +Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags +LFF_spatial_ERC_Visium_spe,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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/spe_filtered_final_with_clusters_and_deconvolution_results.rds,spatialERC_Visium_snRNAseq_spatialLIBD +LFF_spatial_ERC_Visium_pseudobulk_spe,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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_BayesSpace_k09.rds,spatialERC_Visium_snRNAseq_spatialLIBD +LFF_spatial_ERC_Visium_modeling_results,List of modeling results 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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rda,spatialLIBD/spatialLIBD_files/modeling_results_BayesSpace_k09.Rdata,spatialERC_Visium_snRNAseq_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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,FilePath,spatialLIBD/spatialLIBD_files/sce_DLPFC_annotated.zip,spatialERC_Visium_snRNAseq_spatialLIBD +LFF_spatial_ERC_snRNAseq_pseudobulk_spe,Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_BayesSpace_k09.rds,spatialERC_Visium_snRNAseq_spatialLIBD +LFF_spatial_ERC_snRNAseq_modeling_results,List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rda,spatialLIBD/spatialLIBD_files/modeling_results_BayesSpace_k09.Rdata,spatialERC_Visium_snRNAseq_spatialLIBD \ No newline at end of file From 71393cdea847aa9a8116b1f927a4641c8ce2919e Mon Sep 17 00:00:00 2001 From: lahuuki Date: Fri, 21 Nov 2025 16:08:32 +0000 Subject: [PATCH 02/10] Make metadata from scripts --- inst/extdata/metadata_LFF_spatial_ERC.csv | 14 +- inst/scripts/make-metadata_LFF_spatial_ERC.R | 228 +++++++++++++++++++ 2 files changed, 235 insertions(+), 7 deletions(-) create mode 100644 inst/scripts/make-metadata_LFF_spatial_ERC.R diff --git a/inst/extdata/metadata_LFF_spatial_ERC.csv b/inst/extdata/metadata_LFF_spatial_ERC.csv index eb8830d7..8cd266a1 100644 --- a/inst/extdata/metadata_LFF_spatial_ERC.csv +++ b/inst/extdata/metadata_LFF_spatial_ERC.csv @@ -1,7 +1,7 @@ -Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath,Tags -LFF_spatial_ERC_Visium_spe,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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SpatialExperiment,Rds,spatialLIBD/spatialLIBD_files/spe_filtered_final_with_clusters_and_deconvolution_results.rds,spatialERC_Visium_snRNAseq_spatialLIBD -LFF_spatial_ERC_Visium_pseudobulk_spe,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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_BayesSpace_k09.rds,spatialERC_Visium_snRNAseq_spatialLIBD -LFF_spatial_ERC_Visium_modeling_results,List of modeling results 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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rda,spatialLIBD/spatialLIBD_files/modeling_results_BayesSpace_k09.Rdata,spatialERC_Visium_snRNAseq_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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,FilePath,spatialLIBD/spatialLIBD_files/sce_DLPFC_annotated.zip,spatialERC_Visium_snRNAseq_spatialLIBD -LFF_spatial_ERC_snRNAseq_pseudobulk_spe,Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,SingleCellExperiment,Rds,spatialLIBD/spatialLIBD_files/sce_pseudo_BayesSpace_k09.rds,spatialERC_Visium_snRNAseq_spatialLIBD -LFF_spatial_ERC_snRNAseq_modeling_results,List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (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,Mar 17 2023,Homo sapiens,9606,TRUE,LIBD,Leonardo Collado-Torres ,list,Rda,spatialLIBD/spatialLIBD_files/modeling_results_BayesSpace_k09.Rdata,spatialERC_Visium_snRNAseq_spatialLIBD \ No newline at end of file +"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 ","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 ","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 ","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 ","SingleCellExperiment","FilePath","spatialLIBD/spatialLIBD_files/sce_ERC_subcluster.zip","Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD" +"LFF_spatial_ERC_snRNAseq_pseudobulk","Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (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 ","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","List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (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 ","list","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds","Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD" diff --git a/inst/scripts/make-metadata_LFF_spatial_ERC.R b/inst/scripts/make-metadata_LFF_spatial_ERC.R new file mode 100644 index 00000000..dfa834a1 --- /dev/null +++ b/inst/scripts/make-metadata_LFF_spatial_ERC.R @@ -0,0 +1,228 @@ +library("here") +library("sessioninfo") + + +outdir <- "spatialLIBD_files" +pkgname <- "spatialLIBD" + + +meta <- data.frame( + Title = c( + "LFF_spatial_ERC_SRT", + "LFF_spatial_ERC_SRT_pseudobulk", + "LFF_spatial_ERC_SRT_modeling_results", + "LFF_spatial_ERC_snRNAseq", + "LFF_spatial_ERC_snRNAseq_pseudobulk", + "LFF_spatial_ERC_snRNAseq_modeling_results" + ), + Description = c( + "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.", + "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.", + "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.", + "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.", + "Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (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.", + "List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (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." + ), + BiocVersion = "3.17", + Genome = "GRCh38", + SourceType = "GTF", + SourceUrl = "https://bioconductor.org/packages/spatialLIBD", + SourceVersion = "Nov 20 2025", + Species = "Homo sapiens", + TaxonomyId = 9606, + Coordinate_1_based = TRUE, + DataProvider = "LIBD", + Maintainer = "Leonardo Collado-Torres ", + RDataClass = c( + "SpatialExperiment", + "SingleCellExperiment", + "list", + "SingleCellExperiment", + "SingleCellExperiment", + "list" + ), + DispatchClass = c("FilePath", "Rds", "Rds", "FilePath", "Rds", "Rds"), + RDataPath = file.path( + pkgname, + outdir, + c( + "spe_ERC_annotated.zip", + "spe_pseudobulk-SpD.rds", + "modeling_results-SpD.rds", + "sce_ERC_subcluster.zip", + "sce_pseudo_DGE-cell_type_anno.RDS", + "sce_subcluster_modeling_results-cell_type_anno.rds" + ) + ), + Tags = "Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD", + row.names = NULL, + stringsAsFactors = FALSE +) + +write.csv( + meta, + file = here::here("inst", "extdata", "metadata_LFF_spatial_ERC.csv"), + row.names = FALSE +) + +## Check +if (FALSE) { + AnnotationHubData::makeAnnotationHubMetadata(here::here(), fileName = "metadata_LFF_spatial_ERC.csv") +} + +## Reproducibility information +print("Reproducibility information:") +Sys.time() +proc.time() +options(width = 120) +session_info() + +# ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── +# setting value +# version R version 4.2.2 (2022-10-31) +# os macOS Ventura 13.0.1 +# system aarch64, darwin20 +# ui RStudio +# language (EN) +# collate en_US.UTF-8 +# ctype en_US.UTF-8 +# tz America/Mexico_City +# date 2023-02-13 +# rstudio 2022.12.0+353 Elsbeth Geranium (desktop) +# pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) +# +# ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── +# package * version date (UTC) lib source +# AnnotationDbi 1.60.0 2022-11-01 [1] Bioconductor +# AnnotationForge 1.40.0 2022-11-01 [1] Bioconductor +# AnnotationHub 3.6.0 2022-11-01 [1] Bioconductor +# AnnotationHubData 1.28.0 2022-11-01 [1] Bioconductor +# assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) +# Biobase 2.58.0 2022-11-01 [1] Bioconductor +# BiocCheck 1.34.2 2022-11-20 [1] Bioconductor +# BiocFileCache 2.6.0 2022-11-01 [1] Bioconductor +# BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor +# BiocIO 1.8.0 2022-11-01 [1] Bioconductor +# BiocManager 1.30.19 2022-10-25 [1] CRAN (R 4.2.0) +# BiocParallel 1.32.5 2022-12-25 [1] Bioconductor +# BiocVersion 3.16.0 2022-09-20 [1] Bioconductor +# biocViews 1.66.2 2022-12-25 [1] Bioconductor +# biomaRt 2.54.0 2022-11-01 [1] Bioconductor +# Biostrings 2.66.0 2022-11-01 [1] Bioconductor +# bit 4.0.5 2022-11-15 [1] CRAN (R 4.2.2) +# bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0) +# bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0) +# blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0) +# brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0) +# cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0) +# callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2) +# cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0) +# codetools 0.2-19 2023-02-01 [1] CRAN (R 4.2.0) +# colorout 1.2-2 2022-03-01 [1] Github (jalvesaq/colorout@79931fd) +# crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.0) +# curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.0) +# data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.0) +# DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0) +# dbplyr 2.3.0 2023-01-16 [1] CRAN (R 4.2.0) +# DelayedArray 0.24.0 2022-11-01 [1] Bioconductor +# devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.2.0) +# digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0) +# dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.2.0) +# ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) +# evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0) +# fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0) +# fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) +# filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0) +# formatR 1.14 2023-01-17 [1] CRAN (R 4.2.0) +# fs 1.6.0 2023-01-23 [1] CRAN (R 4.2.0) +# futile.logger * 1.4.3 2016-07-10 [1] CRAN (R 4.2.0) +# futile.options 1.0.1 2018-04-20 [1] CRAN (R 4.2.0) +# generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0) +# GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor +# GenomeInfoDbData 1.2.9 2022-11-02 [1] Bioconductor +# GenomicAlignments 1.34.0 2022-11-01 [1] 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────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── From 0dc6d32a944d8f9c2f5ee7d4b88186ff85abd731 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Fri, 21 Nov 2025 16:39:59 +0000 Subject: [PATCH 03/10] Add broad level pb and modeling data too --- inst/extdata/metadata_LFF_spatial_ERC.csv | 6 ++++-- inst/scripts/make-metadata_LFF_spatial_ERC.R | 18 +++++++++++++----- 2 files changed, 17 insertions(+), 7 deletions(-) diff --git a/inst/extdata/metadata_LFF_spatial_ERC.csv b/inst/extdata/metadata_LFF_spatial_ERC.csv index 8cd266a1..1e0324aa 100644 --- a/inst/extdata/metadata_LFF_spatial_ERC.csv +++ b/inst/extdata/metadata_LFF_spatial_ERC.csv @@ -3,5 +3,7 @@ "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 ","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 ","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 ","SingleCellExperiment","FilePath","spatialLIBD/spatialLIBD_files/sce_ERC_subcluster.zip","Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD" -"LFF_spatial_ERC_snRNAseq_pseudobulk","Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (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 ","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","List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (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 ","list","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds","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 ","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 ","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 ","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 ","list","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds","Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD" diff --git a/inst/scripts/make-metadata_LFF_spatial_ERC.R b/inst/scripts/make-metadata_LFF_spatial_ERC.R index dfa834a1..78f821b9 100644 --- a/inst/scripts/make-metadata_LFF_spatial_ERC.R +++ b/inst/scripts/make-metadata_LFF_spatial_ERC.R @@ -12,16 +12,20 @@ meta <- data.frame( "LFF_spatial_ERC_SRT_pseudobulk", "LFF_spatial_ERC_SRT_modeling_results", "LFF_spatial_ERC_snRNAseq", - "LFF_spatial_ERC_snRNAseq_pseudobulk", - "LFF_spatial_ERC_snRNAseq_modeling_results" + "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" ), Description = c( "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.", "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.", "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.", "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.", - "Pseudo-bulked SingleCellExperiment object LFF_spatial_ERC human brain (ERC) snRNA-seq data (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.", - "List of modeling results at the 38 subcluster resolution for the LFF_spatial_ERC human brain (ERC) spatial transcriptomics data (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." + "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.", + "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.", + "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.", + "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." ), BiocVersion = "3.17", Genome = "GRCh38", @@ -39,9 +43,11 @@ meta <- data.frame( "list", "SingleCellExperiment", "SingleCellExperiment", + "SingleCellExperiment", + "list", "list" ), - DispatchClass = c("FilePath", "Rds", "Rds", "FilePath", "Rds", "Rds"), + DispatchClass = c("FilePath", "Rds", "Rds", "FilePath", "Rds", "Rds", "Rds", "Rds"), RDataPath = file.path( pkgname, outdir, @@ -50,7 +56,9 @@ meta <- data.frame( "spe_pseudobulk-SpD.rds", "modeling_results-SpD.rds", "sce_ERC_subcluster.zip", + "sce_pseudo_DGE-cell_type_broad.RDS", "sce_pseudo_DGE-cell_type_anno.RDS", + "sce_subcluster_pseudobulk-cell_type_broad.rds", "sce_subcluster_modeling_results-cell_type_anno.rds" ) ), From 8c46036fab509c78add10bb9642fc3f919d1dfc0 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Tue, 25 Nov 2025 14:55:20 +0000 Subject: [PATCH 04/10] Fix ERC pseudobulk filenames --- inst/extdata/metadata_LFF_spatial_ERC.csv | 4 ++-- inst/scripts/make-metadata_LFF_spatial_ERC.R | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/inst/extdata/metadata_LFF_spatial_ERC.csv b/inst/extdata/metadata_LFF_spatial_ERC.csv index 1e0324aa..35bd3fd7 100644 --- a/inst/extdata/metadata_LFF_spatial_ERC.csv +++ b/inst/extdata/metadata_LFF_spatial_ERC.csv @@ -3,7 +3,7 @@ "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 ","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 ","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 ","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 ","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 ","SingleCellExperiment","Rds","spatialLIBD/spatialLIBD_files/sce_pseudo_DGE-cell_type_anno.RDS","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 ","SingleCellExperiment","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_pseudobulk-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 ","SingleCellExperiment","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_pseudobulk-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 ","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 ","list","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds","Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD" diff --git a/inst/scripts/make-metadata_LFF_spatial_ERC.R b/inst/scripts/make-metadata_LFF_spatial_ERC.R index 78f821b9..c74854cf 100644 --- a/inst/scripts/make-metadata_LFF_spatial_ERC.R +++ b/inst/scripts/make-metadata_LFF_spatial_ERC.R @@ -56,8 +56,8 @@ meta <- data.frame( "spe_pseudobulk-SpD.rds", "modeling_results-SpD.rds", "sce_ERC_subcluster.zip", - "sce_pseudo_DGE-cell_type_broad.RDS", - "sce_pseudo_DGE-cell_type_anno.RDS", + "sce_subcluster_pseudobulk-cell_type_broad.rds", + "sce_subcluster_pseudobulk-cell_type_anno.rds", "sce_subcluster_pseudobulk-cell_type_broad.rds", "sce_subcluster_modeling_results-cell_type_anno.rds" ) From 4b92cce638194c9d5b532067969cd239fbc6a3e0 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Tue, 25 Nov 2025 14:56:43 +0000 Subject: [PATCH 05/10] Add ERC 8 type opttions to fetch_data() --- R/fetch_data.R | 82 ++++++++++++++++++++++++++++++++++++++++++++++- man/fetch_data.Rd | 9 +++++- 2 files changed, 89 insertions(+), 2 deletions(-) diff --git a/R/fetch_data.R b/R/fetch_data.R index 97a75a8b..7989ebe2 100644 --- a/R/fetch_data.R +++ b/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 +294,78 @@ 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/TODO" + } 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/TODO" + } else if (type == "LFF_spatial_ERC_SRT") { + tag <- "LFF_spatial_ERC" + hub_title <- type + + ## While EH is not set-up + file_name <- "spe_pseudobulk-SpD.rds" + url <- + "https://www.dropbox.com/TODO" + } 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/TODO" + } 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/TODO" + } 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/TODO" + } 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/TODO" + } 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/TODO" + } 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/TODO" } file_path <- file.path(destdir, file_name) diff --git a/man/fetch_data.Rd b/man/fetch_data.Rd index 8f40a5b7..ec745af6 100644 --- a/man/fetch_data.Rd +++ b/man/fetch_data.Rd @@ -12,7 +12,14 @@ fetch_data( "Visium_SPG_AD_Visium_wholegenome_spe", "Visium_SPG_AD_Visium_targeted_spe", "Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe", "Visium_SPG_AD_Visium_wholegenome_modeling_results", "visiumStitched_brain_spe", - "visiumStitched_brain_spaceranger", "visiumStitched_brain_Fiji_out"), + "visiumStitched_brain_spaceranger", "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(), bfc = BiocFileCache::BiocFileCache() From 848f120df943bc4119a796e8d3e3da577f778aa2 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Tue, 25 Nov 2025 15:05:18 +0000 Subject: [PATCH 06/10] Update metadata with corrected filenames --- inst/extdata/metadata_LFF_spatial_ERC.csv | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/inst/extdata/metadata_LFF_spatial_ERC.csv b/inst/extdata/metadata_LFF_spatial_ERC.csv index 35bd3fd7..18befc8d 100644 --- a/inst/extdata/metadata_LFF_spatial_ERC.csv +++ b/inst/extdata/metadata_LFF_spatial_ERC.csv @@ -1,9 +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 ","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 ","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 ","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 ","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 ","SingleCellExperiment","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_pseudobulk-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 ","SingleCellExperiment","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_pseudobulk-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 ","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 ","list","Rds","spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds","Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD" +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 ,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 ,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 ,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 ,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 ,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 ,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 ,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 ,list,Rds,spatialLIBD/spatialLIBD_files/sce_subcluster_modeling_results-cell_type_anno.rds,Visium_snRNAseq_AD_Alzheimer_Disease_APOE_ERC_spatialLIBD \ No newline at end of file From 34f4b9b99a1aaa3b9b04ce6f1155be68c4e0b930 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Wed, 26 Nov 2025 12:09:34 +0000 Subject: [PATCH 07/10] Update fetch_data with ERC dropbox links --- R/fetch_data.R | 26 +++++++++----------------- 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/R/fetch_data.R b/R/fetch_data.R index 7989ebe2..abb82747 100644 --- a/R/fetch_data.R +++ b/R/fetch_data.R @@ -301,7 +301,7 @@ fetch_data <- ## While EH is not set-up file_name <- "spe_ERC_annotated.zip" url <- - "https://www.dropbox.com/TODO" + "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 @@ -309,23 +309,15 @@ fetch_data <- ## While EH is not set-up file_name <- "spe_pseudobulk-SpD.rds" url <- - "https://www.dropbox.com/TODO" - } else if (type == "LFF_spatial_ERC_SRT") { - tag <- "LFF_spatial_ERC" - hub_title <- type - - ## While EH is not set-up - file_name <- "spe_pseudobulk-SpD.rds" - url <- - "https://www.dropbox.com/TODO" - } else if (type == "LFF_spatial_ERC_SRT_modeling_results") { + "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/TODO" + "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 @@ -333,7 +325,7 @@ fetch_data <- ## While EH is not set-up file_name <- "sce_ERC_subcluster.zip" url <- - "https://www.dropbox.com/TODO" + "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 @@ -341,7 +333,7 @@ fetch_data <- ## While EH is not set-up file_name <- "sce_subcluster_pseudobulk-cell_type_broad.rds" url <- - "https://www.dropbox.com/TODO" + "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 @@ -349,7 +341,7 @@ fetch_data <- ## While EH is not set-up file_name <- "sce_subcluster_pseudobulk-cell_type_anno.rds" url <- - "https://www.dropbox.com/TODO" + "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 @@ -357,7 +349,7 @@ fetch_data <- ## While EH is not set-up file_name <- "sce_subcluster_pseudobulk-cell_type_broad.rds" url <- - "https://www.dropbox.com/TODO" + "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 @@ -365,7 +357,7 @@ fetch_data <- ## While EH is not set-up file_name <- "sce_subcluster_pseudobulk-cell_type_anno.rds" url <- - "https://www.dropbox.com/TODO" + "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) From 7188cf833ee1756b201d8e95b5db0e10a7526d1f Mon Sep 17 00:00:00 2001 From: lahuuki Date: Wed, 26 Nov 2025 12:17:52 +0000 Subject: [PATCH 08/10] Fix trailing comma --- R/fetch_data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/fetch_data.R b/R/fetch_data.R index abb82747..635a759a 100644 --- a/R/fetch_data.R +++ b/R/fetch_data.R @@ -111,7 +111,7 @@ fetch_data <- "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", + "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster" ), destdir = tempdir(), eh = ExperimentHub::ExperimentHub(), From 9f0cfde88a32ed48dd3c517ca43a8e2bf888415f Mon Sep 17 00:00:00 2001 From: lahuuki Date: Wed, 26 Nov 2025 12:18:04 +0000 Subject: [PATCH 09/10] Update docs --- man/fetch_data.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/fetch_data.Rd b/man/fetch_data.Rd index ec745af6..369a71c2 100644 --- a/man/fetch_data.Rd +++ b/man/fetch_data.Rd @@ -19,7 +19,7 @@ fetch_data( "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", ), + "LFF_spatial_ERC_snRNAseq_modeling_results_subcluster"), destdir = tempdir(), eh = ExperimentHub::ExperimentHub(), bfc = BiocFileCache::BiocFileCache() From 3445b31c5378bb2fdbf81fc08611a4a15a14aa43 Mon Sep 17 00:00:00 2001 From: lahuuki Date: Wed, 26 Nov 2025 14:39:10 +0000 Subject: [PATCH 10/10] Add test for fetch_data(), confirm all dropbox links for ERC data --- tests/testthat/test-fetch_data.R | 46 ++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 tests/testthat/test-fetch_data.R diff --git a/tests/testthat/test-fetch_data.R b/tests/testthat/test-fetch_data.R new file mode 100644 index 00000000..8e27b4ae --- /dev/null +++ b/tests/testthat/test-fetch_data.R @@ -0,0 +1,46 @@ +test_that("multiplication works", { + expect_error(fetch_data(type = "BAD_TYPE")) +}) + + +## test ERC + +# ## SRT data +# spe_erc_path <- fetch_data(type = "LFF_spatial_ERC_SRT") +# spe_erc_path <- unzip(spe_erc_path, exdir = tempdir()) +# spe_erc <- HDF5Array::loadHDF5SummarizedExperiment( +# file.path(tempdir(), "spe_ERC_annotated") +# ) +# spe_erc +# dim: 30494 122202 +# lobstr::obj_size(spe_erc) 3.20 GB +# +# ## SCE data +# sce_erc_path <- fetch_data(type = "LFF_spatial_ERC_snRNAseq") +# sce_erc_path <- unzip(sce_erc_path, exdir = tempdir()) +# sce_erc <- HDF5Array::loadHDF5SummarizedExperiment( +# file.path(tempdir(), "sce_ERC_subcluster") +# ) +# sce_erc +# # dim: 38606 122004 +# # lobstr::obj_size(sce_erc) 258.20 MB +# +# +# erc_simple_types <- c("LFF_spatial_ERC_SRT_pseudobulk", +# "LFF_spatial_ERC_SRT_modeling_results", +# "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") +# +# names(erc_simple_types) <- erc_simple_types +# erc_data_test <- purrr::map(erc_simple_types, fetch_data) +# +# purrr::map_int(erc_data_test, length) +# purrr::map_chr(erc_data_test, class) +# LFF_spatial_ERC_SRT_pseudobulk LFF_spatial_ERC_SRT_modeling_results +# "SpatialExperiment" "list" +# LFF_spatial_ERC_snRNAseq_pseudobulk_broad LFF_spatial_ERC_snRNAseq_pseudobulk_subcluster +# "SingleCellExperiment" "SingleCellExperiment" +# LFF_spatial_ERC_snRNAseq_modeling_results_broad LFF_spatial_ERC_snRNAseq_modeling_results_subcluster +# "list" "list"