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Dataset distribution for Seurat
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Data set ‘pbmcref’ not found when run LoadData("pbmcref") #82

Open MWRR opened 7 months ago

MWRR commented 7 months ago

I am using Seurat v4.4.0 and I was attempting to load pbmcref data. At beginning, I faced an error during loading the data InstallData('pbmcref.SeuratData') this was solved by following #15

but when I run ref <- LoadData("pbmcref") I got the error

Warning message:
In data("pbmcref") : data set ‘pbmcref’ not found

AvailableData()

Dataset Version                                                        Summary    species
adiposeref.SeuratData           adiposeref   1.0.0                                     Azimuth Reference: adipose      human
bmcite.SeuratData                   bmcite   0.3.0                                          30k Bone Marrow Cells      human
bonemarrowref.SeuratData     bonemarrowref   1.0.0                                  Azimuth Reference: bonemarrow      human
cbmc.SeuratData                       cbmc   3.1.4                   scRNAseq and 13-antibody sequencing of CBMCs      human
celegans.embryo.SeuratData celegans.embryo   0.1.0         6k C. elegans embryos from Packer and Zhu et al (2019) C. elegans
fetusref.SeuratData               fetusref   1.0.0                                       Azimuth Reference: fetus      human
hcabm40k.SeuratData               hcabm40k   3.0.0 40,000 Cells From the Human Cell Atlas ICA Bone Marrow Dataset      human
heartref.SeuratData               heartref   1.0.0                                       Azimuth Reference: heart      human
humancortexref.SeuratData   humancortexref   1.0.0                                 Azimuth Reference: humancortex      human
ifnb.SeuratData                       ifnb   3.1.0                              IFNB-Stimulated and Control PBMCs      human
kidneyref.SeuratData             kidneyref   1.0.1                                      Azimuth Reference: kidney      human
lungref.SeuratData                 lungref   2.0.0                                        Azimuth Reference: lung      human
mousecortexref.SeuratData   mousecortexref   1.0.0                                 Azimuth Reference: mousecortex      mouse
panc8.SeuratData                     panc8   3.0.2               Eight Pancreas Datasets Across Five Technologies      human
pancreasref.SeuratData         pancreasref   1.0.0                                    Azimuth Reference: pancreas      human
pbmc3k.SeuratData                   pbmc3k   3.1.4                                     3k PBMCs from 10X Genomics      human
pbmcMultiome.SeuratData       pbmcMultiome   0.1.4                             10X Genomics PBMC Multiome Dataset      human
pbmcref.SeuratData                 pbmcref   1.0.0                                        Azimuth Reference: pbmc      human
pbmcsca.SeuratData                 pbmcsca   3.0.0           Broad Institute PBMC Systematic Comparative Analysis      human
ssHippo.SeuratData                 ssHippo   3.1.4                      Slide-seq v2 dataset of mouse hippocampus      mouse
stxBrain.SeuratData               stxBrain   0.1.1                        10X Genomics Visium Mouse Brain Dataset      mouse
stxKidney.SeuratData             stxKidney   0.1.0                       10X Genomics Visium Mouse Kidney Dataset      mouse
thp1.eccite.SeuratData         thp1.eccite   3.1.5                                               ECCITE-seq THP-1      human
tonsilref.SeuratData             tonsilref   1.0.0                                      Azimuth Reference: tonsil      human
                                      system ncells                                                            tech seurat
adiposeref.SeuratData                adipose 160075                                          scRNA-seq and sNuc-seq   <NA>
bmcite.SeuratData                bone marrow  30672                                                            <NA>  3.2.2
bonemarrowref.SeuratData          bonemarrow 297627                                                          10x v2   <NA>
cbmc.SeuratData            CBMC (cord blood)   8617                                                        CITE-seq  3.1.4
celegans.embryo.SeuratData            embryo   6188                                                            <NA>   <NA>
fetusref.SeuratData                    fetus 377456                                                            <NA>   <NA>
hcabm40k.SeuratData              bone marrow  40000                                                          10x v2   <NA>
heartref.SeuratData                    heart 656509                                          scRNA-seq and sNuc-seq   <NA>
humancortexref.SeuratData       motor cortex  76533                                                            <NA>   <NA>
ifnb.SeuratData                         PBMC  13999                                                          10x v1   <NA>
kidneyref.SeuratData                  kidney  64693                                                            <NA>   <NA>
lungref.SeuratData                      lung 584884                                                            <NA>   <NA>
mousecortexref.SeuratData       motor cortex 159738                                                          10x v3   <NA>
panc8.SeuratData           Pancreatic Islets  14892                SMARTSeq2, Fluidigm C1, CelSeq, CelSeq2, inDrops   <NA>
pancreasref.SeuratData              pancreas  35289                                                            <NA>   <NA>
pbmc3k.SeuratData                       PBMC   2700                                                          10x v1  3.1.4
pbmcMultiome.SeuratData                 pbmc  11909                                                            <NA>  4.1.1
pbmcref.SeuratData                      PBMC   2700                                                          10x v1   <NA>
pbmcsca.SeuratData                      PBMC  31021 10x v2, 10x v3, SMARTSeq2, Seq-Well, inDrops, Drop-seq, CelSeq2   <NA>
ssHippo.SeuratData               hippocampus     NA                                                     slideseq v2   <NA>
stxBrain.SeuratData                    brain  12167                                                          visium   <NA>
stxKidney.SeuratData                  kidney   1438                                                          visium   <NA>
thp1.eccite.SeuratData                  <NA>     NA                                                            <NA>   <NA>
tonsilref.SeuratData                  tonsil 263299                                                          10x v3   <NA>
                           default.dataset disk.datasets                               other.datasets
adiposeref.SeuratData                 <NA>          <NA>                                         <NA>
bmcite.SeuratData                     <NA>          <NA>                                         <NA>
bonemarrowref.SeuratData              <NA>          <NA>                                         <NA>
cbmc.SeuratData                        raw     processed                                         <NA>
celegans.embryo.SeuratData             raw          <NA>                                         <NA>
fetusref.SeuratData                   <NA>          <NA>                                         <NA>
hcabm40k.SeuratData                    raw          <NA>                                         <NA>
heartref.SeuratData                   <NA>          <NA>                                         <NA>
humancortexref.SeuratData             <NA>          <NA>                                         <NA>
ifnb.SeuratData                        raw          <NA>                                    processed
kidneyref.SeuratData                  <NA>          <NA>                                         <NA>
lungref.SeuratData                    <NA>          <NA>                                         <NA>
mousecortexref.SeuratData             <NA>          <NA>                                         <NA>
panc8.SeuratData                       raw          <NA>                                         <NA>
pancreasref.SeuratData                <NA>          <NA>                                         <NA>
pbmc3k.SeuratData                      raw          <NA>                                 pbmc3k.final
pbmcMultiome.SeuratData                 NA          <NA>                          pbmc.rna, pbmc.atac
pbmcref.SeuratData                    <NA>          <NA>                                         <NA>
pbmcsca.SeuratData                     raw          <NA>                                         <NA>
ssHippo.SeuratData                     raw          <NA>                                         <NA>
stxBrain.SeuratData                     NA          <NA> posterior1, posterior2, anterior1, anterior2
stxKidney.SeuratData                   raw          <NA>                                         <NA>
thp1.eccite.SeuratData                <NA>          <NA>                                         <NA>
tonsilref.SeuratData                  <NA>          <NA>                                         <NA>
                                                                                               notes Installed
adiposeref.SeuratData                                                                           <NA>     FALSE
bmcite.SeuratData                                                                               <NA>     FALSE
bonemarrowref.SeuratData                                                                        <NA>     FALSE
cbmc.SeuratData                                                                                 <NA>     FALSE
celegans.embryo.SeuratData                                                                      <NA>     FALSE
fetusref.SeuratData                                                                             <NA>     FALSE
hcabm40k.SeuratData                                                                             <NA>     FALSE
heartref.SeuratData                                                                             <NA>     FALSE
humancortexref.SeuratData                                                                       <NA>     FALSE
ifnb.SeuratData                                                                                 <NA>      TRUE
kidneyref.SeuratData                                                                            <NA>     FALSE
lungref.SeuratData                                                                              <NA>     FALSE
mousecortexref.SeuratData                                                                       <NA>     FALSE
panc8.SeuratData                                                                                <NA>     FALSE
pancreasref.SeuratData                                                                          <NA>     FALSE
pbmc3k.SeuratData                                                                               <NA>     FALSE
pbmcMultiome.SeuratData                                 One sample with two modalities, RNA and ATAC     FALSE
pbmcref.SeuratData                                                                              <NA>      TRUE
pbmcsca.SeuratData                                                                     HCA benchmark     FALSE
ssHippo.SeuratData                                                                              <NA>     FALSE
stxBrain.SeuratData        One sample split across four datasets as paired anterior/posterior slices     FALSE
stxKidney.SeuratData                                                                            <NA>     FALSE
thp1.eccite.SeuratData                                                                          <NA>     FALSE
tonsilref.SeuratData                                                                            <NA>     FALSE
                           InstalledVersion
adiposeref.SeuratData                  <NA>
bmcite.SeuratData                      <NA>
bonemarrowref.SeuratData               <NA>
cbmc.SeuratData                        <NA>
celegans.embryo.SeuratData             <NA>
fetusref.SeuratData                    <NA>
hcabm40k.SeuratData                    <NA>
heartref.SeuratData                    <NA>
humancortexref.SeuratData              <NA>
ifnb.SeuratData                       3.0.0
kidneyref.SeuratData                   <NA>
lungref.SeuratData                     <NA>
mousecortexref.SeuratData              <NA>
panc8.SeuratData                       <NA>
pancreasref.SeuratData                 <NA>
pbmc3k.SeuratData                      <NA>
pbmcMultiome.SeuratData                <NA>
pbmcref.SeuratData                    1.0.0
pbmcsca.SeuratData                     <NA>
ssHippo.SeuratData                     <NA>
stxBrain.SeuratData                    <NA>
stxKidney.SeuratData                   <NA>
thp1.eccite.SeuratData                 <NA>
tonsilref.SeuratData                   <NA>

sessionInfo()

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8    LC_MONETARY=English_Australia.utf8
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.utf8    

time zone: Australia/Sydney
tzcode source: internal

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

other attached packages:
[1] ifnb.SeuratData_3.0.0    patchwork_1.2.0          pbmcref.SeuratData_1.0.0 SeuratData_0.2.2.9001   
[5] SeuratObject_5.0.1       Seurat_4.4.0            

loaded via a namespace (and not attached):
  [1] deldir_2.0-2           pbapply_1.7-2          gridExtra_2.3          rlang_1.1.2            magrittr_2.0.3        
  [6] RcppAnnoy_0.0.21       matrixStats_1.2.0      ggridges_0.5.5         compiler_4.3.2         spatstat.geom_3.2-7   
 [11] png_0.1-8              vctrs_0.6.5            reshape2_1.4.4         stringr_1.5.1          crayon_1.5.2          
 [16] pkgconfig_2.0.3        fastmap_1.1.1          ellipsis_0.3.2         utf8_1.2.4             promises_1.2.1        
 [21] purrr_1.0.2            jsonlite_1.8.8         goftest_1.2-3          later_1.3.2            spatstat.utils_3.0-4  
 [26] irlba_2.3.5.1          parallel_4.3.2         cluster_2.1.6          R6_2.5.1               ica_1.0-3             
 [31] stringi_1.8.3          RColorBrewer_1.1-3     spatstat.data_3.0-3    reticulate_1.34.0      parallelly_1.36.0     
 [36] lmtest_0.9-40          scattermore_1.2        Rcpp_1.0.12            tensor_1.5             future.apply_1.11.1   
 [41] zoo_1.8-12             sctransform_0.4.1      httpuv_1.6.13          Matrix_1.6-4           splines_4.3.2         
 [46] igraph_1.6.0           tidyselect_1.2.0       abind_1.4-5            spatstat.random_3.2-2  codetools_0.2-19      
 [51] miniUI_0.1.1.1         spatstat.explore_3.2-5 listenv_0.9.0          lattice_0.22-5         tibble_3.2.1          
 [56] plyr_1.8.9             shiny_1.8.0            ROCR_1.0-11            Rtsne_0.17             future_1.33.1         
 [61] survival_3.5-7         polyclip_1.10-6        fitdistrplus_1.1-11    pillar_1.9.0           KernSmooth_2.23-22    
 [66] plotly_4.10.3          generics_0.1.3         sp_2.1-2               ggplot2_3.4.4          munsell_0.5.0         
 [71] scales_1.3.0           globals_0.16.2         xtable_1.8-4           glue_1.7.0             lazyeval_0.2.2        
 [76] tools_4.3.2            data.table_1.14.10     RANN_2.6.1             leiden_0.4.3.1         dotCall64_1.1-1       
 [81] cowplot_1.1.2          grid_4.3.2             tidyr_1.3.0            colorspace_2.1-0       nlme_3.1-164          
 [86] cli_3.6.2              rappdirs_0.3.3         spatstat.sparse_3.0-3  spam_2.10-0            fansi_1.0.6           
 [91] viridisLite_0.4.2      dplyr_1.1.4            uwot_0.1.16            gtable_0.3.4           digest_0.6.33         
 [96] progressr_0.14.0       ggrepel_0.9.4          htmlwidgets_1.6.4      htmltools_0.5.7        lifecycle_1.0.4       
[101] httr_1.4.7             mime_0.12              MASS_7.3-60
MarcElosua commented 3 months ago

Same here!

ozgunerdogan commented 3 months ago

Same problem for lungref, it is installed but I cannot load it with either data("lungref") or LoadData("lungref")

royfrancis commented 3 weeks ago

Same here:

r$> InstalledData()
                   Dataset Version                 Summary
pbmcref.SeuratData pbmcref   1.0.0 Azimuth Reference: pbmc
                   species system ncells   tech seurat
pbmcref.SeuratData   human   PBMC   2700 10x v1   <NA>
                   default.dataset disk.datasets
pbmcref.SeuratData            <NA>          <NA>
                   other.datasets notes Installed
pbmcref.SeuratData           <NA>  <NA>      TRUE
                   InstalledVersion
pbmcref.SeuratData            1.0.0
r$> data("pbmcref")
Warning message:
In data("pbmcref") : data set ‘pbmcref’ not found
r$> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

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

other attached packages:
 [1] pbmcref.SeuratData_1.0.0 scPred_1.9.2            
 [3] SeuratData_0.2.2.9001    dplyr_1.1.4             
 [5] tidyr_1.3.1              patchwork_1.2.0         
 [7] ggplot2_3.5.1            stringr_1.5.1           
 [9] readxl_1.4.3             knitr_1.48              
[11] Seurat_5.1.0             SeuratObject_5.0.2      
[13] sp_2.1-4