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20 hours ago •
satijalab
satijalab
Data set ‘pbmcref’ not found when run LoadData("pbmcref")
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
Same problem for lungref, it is installed but I cannot load it with either data("lungref") or LoadData("lungref")
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
