Dataset not found with LoadData but it is installed

[MartaBenegas]

Hi, I was trying to use the SeuratData package. I've installed the package, looked at the available data, and installed it with the "Dataset" name. However, I'm not able to load the Azimuth datasets:

> library(SeuratData)
Registered S3 methods overwritten by 'htmltools':
  method               from         
  print.html           tools:rstudio
  print.shiny.tag      tools:rstudio
  print.shiny.tag.list tools:rstudio
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
── Installed datasets ────────────────────────────────────────────────────────────────────────────────────────────────────────────── SeuratData v0.2.2.9001 ──
✔ adiposeref    1.0.0                                                          ✔ hcabm40k      3.0.0
✔ bonemarrowref 1.0.0                                                          ✔ pbmcsca       3.0.0

───────────────────────────────────────────────────────────────────────────── Key ────────────────────────────────────────────────────────────────────────────
✔ Dataset loaded successfully
❯ Dataset built with a newer version of Seurat than installed
❓ Unknown version of Seurat installed

> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp

Attaching package: ‘SeuratObject’

The following object is masked from ‘package:base’:

    intersect

> 
> LoadData("adiposeref")
Error: Could not find dataset 'adiposeref', please check manifest and try again
> data("adiposeref")
Warning: data set ‘adiposeref’ not found
> LoadData("bonemarrowref")
Error: Could not find dataset 'bonemarrowref', please check manifest and try again
> data("bonemarrowref")
Warning: data set ‘bonemarrowref’ not found

And the datasets that are not in Azimuth don't seem to have annotations:

> LoadData("hcabm40k")
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Warning: Assay RNA changing from Assay to AssayEnsuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in RNA
Validating object structure for Assay ‘RNA’
Object representation is consistent with the most current Seurat version
Warning: Assay RNA changing from Assay to Assay5An object of class Seurat 
17369 features across 40000 samples within 1 assay 
Active assay: RNA (17369 features, 0 variable features)
 2 layers present: counts, data

> head(hcabm40k@meta.data)
                                     orig.ident nCount_RNA nFeature_RNA
MantonBM1_HiSeq_8-CCCAATCGTATGCTTG-1  MantonBM1       3235          856
MantonBM1_HiSeq_8-CTGCTGTAGGACACCA-1  MantonBM1       1566          653
MantonBM1_HiSeq_3-CAGCTGGGTACATGTC-1  MantonBM1       2103          716
MantonBM1_HiSeq_7-GCTTCCAAGATGTAAC-1  MantonBM1       1798          750
MantonBM1_HiSeq_6-AGTGAGGCAGGGTTAG-1  MantonBM1      11540         2760
MantonBM1_HiSeq_5-ATGTGTGCACCGAATT-1  MantonBM1      25616         1966

[xcpanda]

I got the same Error when I used LoadData("bonemarrowref").
I've tried SeuratData v0.2.2.9001 (with Seurat v5.0.1) and SeuratData v0.2.1 (with Seurat v4.1.1), but none worked.
Hoping for any suggestions.

[FanRongRong98]

library(Azimuth)
bonemarrowref <- LoadData("bonemarrowref", "azimuth")

[MartaBenegas]

Thanks! It worked.

However, I'm not able to find the slot with counts. It seems that the bonemarrowref$map@assays$refAssay@data is composed entirely of 0. Is this expected? Where can I find the counts?

> all(bonemarrowref$map@assays$refAssay@data == 0)
[1] TRUE

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=es_ES.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=es_ES.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=es_ES.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Madrid
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pbmcsca.SeuratData_3.0.0       ifnb.SeuratData_3.1.0          hcabm40k.SeuratData_3.0.0      bonemarrowref.SeuratData_1.0.0
 [5] adiposeref.SeuratData_1.0.0    SeuratData_0.2.2.9001          scuttle_1.11.3                 SingleCellExperiment_1.24.0   
 [9] gdata_3.0.0                    anndata_0.7.5.6                Azimuth_0.5.0                  shinyBS_0.61.1                
[13] Seurat_5.0.1                   SeuratObject_5.0.1             sp_2.1-2                       SingleR_2.4.0                 
[17] SummarizedExperiment_1.32.0    Biobase_2.62.0                 GenomicRanges_1.54.1           GenomeInfoDb_1.38.5           
[21] IRanges_2.36.0                 S4Vectors_0.40.2               BiocGenerics_0.48.1            MatrixGenerics_1.14.0         
[25] matrixStats_1.2.0             

loaded via a namespace (and not attached):
  [1] fs_1.6.3                          ProtGenerics_1.34.0               spatstat.sparse_3.0-3             bitops_1.0-7                     
  [5] DirichletMultinomial_1.44.0       TFBSTools_1.40.0                  httr_1.4.7                        RColorBrewer_1.1-3               
  [9] tools_4.3.2                       sctransform_0.4.1                 utf8_1.2.4                        R6_2.5.1                         
 [13] DT_0.31                           lazyeval_0.2.2                    uwot_0.1.16                       rhdf5filters_1.14.1              
 [17] withr_2.5.2                       prettyunits_1.2.0                 gridExtra_2.3                     progressr_0.14.0                 
 [21] cli_3.6.2                         Cairo_1.6-2                       spatstat.explore_3.2-5            fastDummies_1.7.3                
 [25] EnsDb.Hsapiens.v86_2.99.0         shinyjs_2.1.0                     labeling_0.4.3                    spatstat.data_3.0-3              
 [29] readr_2.1.5                       ggridges_0.5.5                    pbapply_1.7-2                     Rsamtools_2.18.0                 
 [33] R.utils_2.12.3                    parallelly_1.36.0                 BSgenome_1.70.1                   rstudioapi_0.15.0                
 [37] RSQLite_2.3.4                     generics_0.1.3                    BiocIO_1.12.0                     gtools_3.9.5                     
 [41] ica_1.0-3                         spatstat.random_3.2-2             googlesheets4_1.1.1               dplyr_1.1.4                      
 [45] GO.db_3.18.0                      Matrix_1.6-4                      ggbeeswarm_0.7.2                  fansi_1.0.6                      
 [49] abind_1.4-5                       R.methodsS3_1.8.2                 lifecycle_1.0.4                   yaml_2.3.8                       
 [53] rhdf5_2.46.1                      SparseArray_1.2.3                 BiocFileCache_2.10.1              Rtsne_0.17                       
 [57] grid_4.3.2                        blob_1.2.4                        promises_1.2.1                    shinydashboard_0.7.2             
 [61] crayon_1.5.2                      miniUI_0.1.1.1                    lattice_0.22-5                    beachmat_2.18.0                  
 [65] cowplot_1.1.2                     annotate_1.80.0                   GenomicFeatures_1.54.1            KEGGREST_1.42.0                  
 [69] pillar_1.9.0                      knitr_1.45                        rjson_0.2.21                      future.apply_1.11.1              
 [73] codetools_0.2-19                  fastmatch_1.1-4                   leiden_0.4.3.1                    glue_1.7.0                       
 [77] data.table_1.14.10                vctrs_0.6.5                       png_0.1-8                         spam_2.10-0                      
 [81] cellranger_1.1.0                  poweRlaw_0.70.6                   gtable_0.3.4                      assertthat_0.2.1                 
 [85] cachem_1.0.8                      xfun_0.41                         Signac_1.12.0                     S4Arrays_1.2.0                   
 [89] mime_0.12                         pracma_2.4.4                      survival_3.5-7                    gargle_1.5.2                     
 [93] RcppRoll_0.3.0                    ellipsis_0.3.2                    fitdistrplus_1.1-11               ROCR_1.0-11                      
 [97] nlme_3.1-163                      bit64_4.0.5                       progress_1.2.3                    filelock_1.0.3                   
[101] RcppAnnoy_0.0.21                  irlba_2.3.5.1                     vipor_0.4.5                       KernSmooth_2.23-22               
[105] SeuratDisk_0.0.0.9021             colorspace_2.1-0                  seqLogo_1.68.0                    DBI_1.2.0                        
[109] ggrastr_1.0.2                     tidyselect_1.2.0                  bit_4.0.5                         compiler_4.3.2                   
[113] curl_5.2.0                        hdf5r_1.3.8                       xml2_1.3.6                        DelayedArray_0.28.0              
[117] plotly_4.10.3                     rtracklayer_1.62.0                scales_1.3.0                      caTools_1.18.2                   
[121] lmtest_0.9-40                     rappdirs_0.3.3                    stringr_1.5.1                     digest_0.6.33                    
[125] goftest_1.2-3                     presto_1.0.0                      spatstat.utils_3.0-4              XVector_0.42.0                   
[129] htmltools_0.5.7                   pkgconfig_2.0.3                   sparseMatrixStats_1.14.0          dbplyr_2.4.0                     
[133] fastmap_1.1.1                     ensembldb_2.26.0                  rlang_1.1.3                       htmlwidgets_1.6.4                
[137] shiny_1.8.0                       DelayedMatrixStats_1.24.0         farver_2.1.1                      zoo_1.8-12                       
[141] jsonlite_1.8.8                    BiocParallel_1.36.0               R.oo_1.25.0                       BiocSingular_1.18.0              
[145] RCurl_1.98-1.14                   magrittr_2.0.3                    GenomeInfoDbData_1.2.11           dotCall64_1.1-1                  
[149] patchwork_1.2.0                   Rhdf5lib_1.24.1                   munsell_0.5.0                     Rcpp_1.0.12                      
[153] reticulate_1.34.0                 stringi_1.8.3                     zlibbioc_1.48.0                   MASS_7.3-60                      
[157] plyr_1.8.9                        parallel_4.3.2                    listenv_0.9.0                     ggrepel_0.9.5                    
[161] deldir_2.0-2                      CNEr_1.38.0                       Biostrings_2.70.1                 splines_4.3.2                    
[165] tensor_1.5                        hms_1.1.3                         BSgenome.Hsapiens.UCSC.hg38_1.4.5 igraph_1.6.0                     
[169] spatstat.geom_3.2-7               RcppHNSW_0.5.0                    reshape2_1.4.4                    biomaRt_2.58.0                   
[173] ScaledMatrix_1.10.0               TFMPvalue_0.0.9                   XML_3.99-0.16                     JASPAR2020_0.99.10               
[177] tzdb_0.4.0                        httpuv_1.6.13                     RANN_2.6.1                        tidyr_1.3.0                      
[181] purrr_1.0.2                       polyclip_1.10-6                   future_1.33.1                     scattermore_1.2                  
[185] ggplot2_3.4.4                     rsvd_1.0.5                        xtable_1.8-4                      restfulr_0.0.15                  
[189] AnnotationFilter_1.26.0           RSpectra_0.16-1                   later_1.3.2                       googledrive_2.1.1                
[193] viridisLite_0.4.2                 tibble_3.2.1                      beeswarm_0.4.0                    memoise_2.0.1                    
[197] AnnotationDbi_1.64.1              GenomicAlignments_1.38.1          cluster_2.1.5                     globals_0.16.2   

[vd4mmind]

I am having the same issues. Is there a better way now? I am unable to install both Azimuth and signac as mentioned in the VIgnette. Is there a workaround?

devtools::install_github("satijalab/azimuth", "seurat5")
Downloading GitHub repo satijalab/azimuth@seurat5
Error: Failed to install 'Azimuth' from GitHub:
  HTTP error 404.
  No commit found for the ref seurat5

  Did you spell the repo owner (`stuart-lab`) and repo name (`signac`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.
> remotes::install_github("stuart-lab/signac", "seurat5", quiet = TRUE)
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 404.
  No commit found for the ref seurat5

  Did you spell the repo owner (`stuart-lab`) and repo name (`signac`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.

> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pbmc3k.SeuratData_3.1.4     patchwork_1.2.0             ggplot2_3.5.0               SeuratWrappers_0.3.2        SeuratData_0.2.2.9001      
 [6] dplyr_1.1.4                 SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 Biobase_2.58.0              GenomicRanges_1.50.2       
[11] GenomeInfoDb_1.34.9         IRanges_2.32.0              S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0      
[16] matrixStats_1.2.0           scFlow_0.7.4                DoubletFinder_2.0.4         EWCE_1.6.0                  RNOmni_1.0.1.2             
[21] apcluster_1.4.11            lme4_1.1-35.1               Seurat_5.0.2                SeuratObject_5.0.1          sp_2.1-3                   
[26] irlba_2.3.5.1               Matrix_1.6-5               

loaded via a namespace (and not attached):
  [1] rsvd_1.0.5                    ica_1.0-3                     svglite_2.1.3                 ps_1.7.6                      foreach_1.5.2                
  [6] lmtest_0.9-40                 crayon_1.5.2                  MASS_7.3-58.2                 rhdf5filters_1.10.1           MAST_1.24.1                  
 [11] WriteXLS_6.5.0                nlme_3.1-162                  backports_1.4.1               monocle3_1.3.5                rlang_1.1.3                  
 [16] XVector_0.38.0                bib2df_1.1.2.0                ROCR_1.0-11                   callr_3.7.5                   nloptr_2.0.3                 
 [21] limma_3.54.2                  scater_1.26.1                 filelock_1.0.3                stringfish_0.16.0             qs_0.25.7                    
 [26] rjson_0.2.21                  BiocParallel_1.32.6           bit64_4.0.5                   glue_1.7.0                    rngtools_1.5.2               
 [31] sctransform_0.4.1             processx_3.8.3                parallel_4.2.3                vipor_0.4.7                   spatstat.sparse_3.0-3        
 [36] AnnotationDbi_1.60.2          UpSetR_1.4.0                  HGNChelper_0.8.1              dotCall64_1.1-1               spatstat.geom_3.2-9          
 [41] tidyselect_1.2.0              usethis_2.2.2                 fitdistrplus_1.1-11           XML_3.99-0.16.1               tidyr_1.3.1                  
 [46] zoo_1.8-12                    ggpubr_0.6.0                  formattable_0.2.1             xtable_1.8-4                  RcppHNSW_0.6.0               
 [51] magrittr_2.0.3                evaluate_0.23                 scuttle_1.8.4                 cli_3.6.2                     zlibbioc_1.44.0              
 [56] rstudioapi_0.15.0             doRNG_1.8.6                   miniUI_0.1.1.1                whisker_0.4.1                 treeio_1.22.0                
 [61] rliger_1.0.1                  fastDummies_1.7.3             shiny_1.8.0                   xfun_0.42                     BiocSingular_1.14.0          
 [66] pkgbuild_1.4.3                cluster_2.1.4                 KEGGREST_1.38.0               tibble_3.2.1                  interactiveDisplayBase_1.36.0
 [71] ggrepel_0.9.5                 threejs_0.3.3                 ape_5.7-1                     listenv_0.9.1                 Biostrings_2.66.0            
 [76] png_0.1-8                     future_1.33.1                 withr_3.0.0                   bitops_1.0-7                  plyr_1.8.9                   
 [81] dqrng_0.3.2                   RcppParallel_5.1.7            pillar_1.9.0                  cachem_1.0.8                  fs_1.6.3                     
 [86] hdf5r_1.3.9                   paletteer_1.6.0               DelayedMatrixStats_1.20.0     vctrs_0.6.5                   ellipsis_0.3.2               
 [91] generics_0.1.3                RApiSerialize_0.1.2           devtools_2.4.5                tools_4.2.3                   beeswarm_0.4.0               
 [96] munsell_0.5.0                 DelayedArray_0.24.0           fastmap_1.1.1                 compiler_4.2.3                pkgload_1.3.4                
[101] abind_1.4-5                   httpuv_1.6.14                 ExperimentHub_2.6.0           sessioninfo_1.2.2             ewceData_1.6.0               
[106] plotly_4.10.4.9000            GenomeInfoDbData_1.2.9        gridExtra_2.3                 enrichR_3.2                   edgeR_3.40.2                 
[111] lattice_0.20-45               deldir_2.0-4                  utf8_1.2.4                    later_1.3.2                   BiocFileCache_2.6.1          
[116] humaniformat_0.6.0            jsonlite_1.8.8                kBET_0.99.6                   scales_1.3.0                  ScaledMatrix_1.6.0           
[121] tidytree_0.4.6                pbapply_1.7-2                 carData_3.0-5                 sparseMatrixStats_1.10.0      renv_1.0.3                   
[126] lazyeval_0.2.2                promises_1.2.1                car_3.1-2                     doParallel_1.0.17             R.utils_2.12.3               
[131] goftest_1.2-3                 spatstat.utils_3.0-4          reticulate_1.35.0             rmarkdown_2.25                sandwich_3.1-0               
[136] cowplot_1.1.3                 forcats_1.0.0                 Rtsne_0.17                    uwot_0.1.16.9000              igraph_2.0.2                 
[141] HDF5Array_1.26.0              survival_3.5-3                yaml_2.3.8                    systemfonts_1.0.5             htmltools_0.5.7              
[146] memoise_2.0.1                 profvis_0.3.8                 locfit_1.5-9.8                viridisLite_0.4.2             digest_0.6.34                
[151] assertthat_0.2.1              mime_0.12                     rappdirs_0.3.3                spam_2.10-0                   RSQLite_2.3.5                
[156] yulab.utils_0.1.4             future.apply_1.11.1           remotes_2.4.2.1               orthogene_1.4.2               data.table_1.15.2            
[161] urlchecker_1.0.1              blob_1.2.4                    R.oo_1.26.0                   preprocessCore_1.60.2         splines_4.2.3                
[166] Formula_1.2-5                 rematch2_2.1.2                Rhdf5lib_1.20.0               AnnotationHub_3.6.0           RCurl_1.98-1.14              
[171] broom_1.0.5                   hms_1.1.3                     gprofiler2_0.2.3              base64enc_0.1-3               rhdf5_2.42.1                 
[176] colorspace_2.1-0              DropletUtils_1.18.1           BiocManager_1.30.22           WebGestaltR_0.4.6             ggbeeswarm_0.7.2             
[181] aplot_0.2.2                   maxLik_1.5-2                  mclust_6.1                    Rcpp_1.0.12                   RANN_2.6.1                   
[186] fansi_1.0.6                   tzdb_0.4.0                    parallelly_1.37.1             R6_2.5.1                      grid_4.2.3                   
[191] ggridges_0.5.6                lifecycle_1.0.4               miscTools_0.6-28              curl_5.2.0                    ggsignif_0.6.4               
[196] minqa_1.2.6                   leaflet_2.2.1                 leiden_0.4.3.1                desc_1.4.3                    RcppAnnoy_0.0.22             
[201] RColorBrewer_1.1-3            iterators_1.0.14              spatstat.explore_3.2-6        stringr_1.5.1                 htmlwidgets_1.6.4            
[206] beachmat_2.14.2               polyclip_1.10-6               biomaRt_2.54.1                purrr_1.0.2                   crosstalk_1.2.1              
[211] DirichletReg_0.7-1            gridGraphics_0.5-1            globals_0.16.2                spatstat.random_3.2-3         progressr_0.14.0             
[216] codetools_0.2-19              FNN_1.1.4                     prettyunits_1.2.0             dbplyr_2.4.0                  RSpectra_0.16-1              
[221] R.methodsS3_1.8.2             gtable_0.3.4                  DBI_1.2.2                     ggfun_0.1.4                   tensor_1.5                   
[226] httr_1.4.7                    KernSmooth_2.23-20            stringi_1.8.3                 progress_1.2.3                english_1.2-6                
[231] reshape2_1.4.4                viridis_0.6.5                 ggtree_3.6.2                  xml2_1.3.6                    ggdendro_0.2.0               
[236] boot_1.3-28.1                 grr_0.9.5                     BiocNeighbors_1.16.0          readr_2.1.5                   ggplotify_0.1.2              
[241] homologene_1.4.68.19.3.27     scattermore_1.2               BiocVersion_3.16.0            bit_4.0.5                     spatstat.data_3.0-4          
[246] pkgconfig_2.0.3               babelgene_22.9                rstatix_0.7.2                 knitr_1.45   

[FanRongRong98]

@MartaBenegas I didn't find the slot either. I intend to download the raw data and process it into count myself. If you find the slot with counts, please tell me where it is.

[MartaBenegas]

@FanRongRong98 Unfortunately I haven't been able to find the counts in any Azimuth dataset I've tried.

@mojaveazure and team, is it possible to somehow retrieve the counts or are you planning to include them? I think it would be very helpful!