2 Usage

library(SFEData)

Example spatial transcriptomics datasets with Simple Features annotations as SpatialFeatureExperiment objects. These are the datasets available from this package and functions to download the datasets:

Visium:

Full Visium dataset of the first time point, including spots outside tissue (McKellarMuscleData())
Small subset of the full Visium dataset for function examples. (McKellarMuscleData())
A second small subset of the full Visium dataset with a different sample_id used for function examples involving multiple samples (McKellarMuscleData())

Slide-seq2:

Slide-seq2 human melanoma brain metastasis dataset (BiermannMelaMetasData())
Slide-seq2 human melanoma extracranial metastasis dataset (BiermannMelaMetasData())

Xenium:

10X Xenium formalin fixed paraffin embedded (FFPE) Xenium dataset for human breast cancer (2 biological replica, JanesickBreastData())

CosMX:

Nanostring CosMX FFPE human non small cell lung cancer data (HeNSCLCData())

MERFISH:

Vizgen MERFISH mouse liver data (VizgenLiverData)

This package is used extensively in examples and vignettes of the SpatialFeatureExperiment and Voyager packages. The same function is used for different samples from the same study, and the dataset argument determines which sample is downloaded:

sfe <- McKellarMuscleData(dataset = "small")
#> snapshotDate(): 2022-10-24
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
#> require("SpatialFeatureExperiment")

sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.5 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] SpatialFeatureExperiment_1.0.0 SFEData_1.0.2                 
#> [3] BiocStyle_2.26.0              
#> 
#> loaded via a namespace (and not attached):
#>   [1] SpatialExperiment_1.8.0       deldir_1.0-6                 
#>   [3] rjson_0.2.21                  ellipsis_0.3.2               
#>   [5] class_7.3-20                  scuttle_1.8.0                
#>   [7] XVector_0.38.0                GenomicRanges_1.50.0         
#>   [9] proxy_0.4-27                  bit64_4.0.5                  
#>  [11] interactiveDisplayBase_1.36.0 AnnotationDbi_1.60.0         
#>  [13] fansi_1.0.3                   codetools_0.2-18             
#>  [15] R.methodsS3_1.8.2             sparseMatrixStats_1.10.0     
#>  [17] cachem_1.0.6                  knitr_1.40                   
#>  [19] jsonlite_1.8.3                dbplyr_2.2.1                 
#>  [21] png_0.1-7                     R.oo_1.25.0                  
#>  [23] shiny_1.7.3                   HDF5Array_1.26.0             
#>  [25] BiocManager_1.30.19           compiler_4.2.1               
#>  [27] httr_1.4.4                    dqrng_0.3.0                  
#>  [29] assertthat_0.2.1              Matrix_1.5-1                 
#>  [31] fastmap_1.1.0                 limma_3.54.0                 
#>  [33] cli_3.4.1                     s2_1.1.0                     
#>  [35] later_1.3.0                   htmltools_0.5.3              
#>  [37] tools_4.2.1                   glue_1.6.2                   
#>  [39] GenomeInfoDbData_1.2.9        dplyr_1.0.10                 
#>  [41] wk_0.7.0                      rappdirs_0.3.3               
#>  [43] Rcpp_1.0.9                    Biobase_2.58.0               
#>  [45] jquerylib_0.1.4               vctrs_0.5.0                  
#>  [47] Biostrings_2.66.0             rhdf5filters_1.10.0          
#>  [49] spdep_1.2-7                   ExperimentHub_2.6.0          
#>  [51] DelayedMatrixStats_1.20.0     xfun_0.34                    
#>  [53] stringr_1.4.1                 beachmat_2.14.0              
#>  [55] mime_0.12                     lifecycle_1.0.3              
#>  [57] AnnotationHub_3.6.0           edgeR_3.40.0                 
#>  [59] zlibbioc_1.44.0               promises_1.2.0.1             
#>  [61] MatrixGenerics_1.10.0         parallel_4.2.1               
#>  [63] SummarizedExperiment_1.28.0   rhdf5_2.42.0                 
#>  [65] SingleCellExperiment_1.20.0   yaml_2.3.6                   
#>  [67] curl_4.3.3                    memoise_2.0.1                
#>  [69] sass_0.4.2                    stringi_1.7.8                
#>  [71] RSQLite_2.2.18                BiocVersion_3.16.0           
#>  [73] S4Vectors_0.36.0              e1071_1.7-12                 
#>  [75] BiocGenerics_0.44.0           filelock_1.0.2               
#>  [77] boot_1.3-28                   BiocParallel_1.32.0          
#>  [79] spData_2.2.0                  GenomeInfoDb_1.34.0          
#>  [81] rlang_1.0.6                   pkgconfig_2.0.3              
#>  [83] matrixStats_0.62.0            bitops_1.0-7                 
#>  [85] evaluate_0.17                 lattice_0.20-45              
#>  [87] purrr_0.3.5                   Rhdf5lib_1.20.0              
#>  [89] sf_1.0-8                      bit_4.0.4                    
#>  [91] tidyselect_1.2.0              magrittr_2.0.3               
#>  [93] bookdown_0.29                 R6_2.5.1                     
#>  [95] IRanges_2.32.0                magick_2.7.3                 
#>  [97] generics_0.1.3                DelayedArray_0.24.0          
#>  [99] DBI_1.1.3                     pillar_1.8.1                 
#> [101] withr_2.5.0                   units_0.8-0                  
#> [103] sp_1.5-0                      KEGGREST_1.38.0              
#> [105] RCurl_1.98-1.9                tibble_3.1.8                 
#> [107] crayon_1.5.2                  DropletUtils_1.18.0          
#> [109] KernSmooth_2.23-20            utf8_1.2.2                   
#> [111] BiocFileCache_2.6.0           rmarkdown_2.17               
#> [113] locfit_1.5-9.6                grid_4.2.1                   
#> [115] blob_1.2.3                    digest_0.6.30                
#> [117] classInt_0.4-8                xtable_1.8-4                 
#> [119] httpuv_1.6.6                  R.utils_2.12.1               
#> [121] stats4_4.2.1                  bslib_0.4.0

Example SpatialFeatureExperiment datasets

3 November 2022

Contents

1 Installation

2 Usage