Open MartaBenegas opened 11 months ago
xcpanda
commented
11 months ago 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
commented
11 months ago library(Azimuth) bonemarrowref <- LoadData("bonemarrowref", "azimuth")
MartaBenegas
commented
9 months ago 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
commented
8 months ago 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 @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
commented
8 months ago @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!
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:
And the datasets that are not in Azimuth don't seem to have annotations: