This package can be installed from Bioconductor with the following command:
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:
McKellarMuscleData())McKellarMuscleData())sample_id used for function examples involving multiple
samples (McKellarMuscleData())Slide-seq2:
BiermannMelaMetasData())BiermannMelaMetasData())Xenium:
JanesickBreastData())CosMX:
HeNSCLCData())CosMXOutput())MERFISH:
VizgenLiverData())VizgenOutput())seqFISH:
LohoffGastrulationData())Xenium: * Xenium output subset of mouse brain data
(XeniumOutput())
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")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> require("SpatialFeatureExperiment")The outputs (in *Output()) are not SFE objects, but a
small subset in the format of the standard output of the technology,
used to unit test read functions. Where the files are saved is
controlled by the file_path argument.
(fp <- CosMXOutput(file_path = "foo"))
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> The downloaded files are in /tmp/RtmpHpT4RA/Rbuild1bd767fbdf0e/SFEData/vignettes/foo/cosmx
#> [1] "/tmp/RtmpHpT4RA/Rbuild1bd767fbdf0e/SFEData/vignettes/foo/cosmx"sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04.1 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [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
#>
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] SpatialFeatureExperiment_1.15.1 SFEData_1.15.0
#> [3] BiocStyle_2.41.0
#>
#> loaded via a namespace (and not attached):
#> [1] sys_3.4.3 jsonlite_2.0.0
#> [3] wk_0.9.5 magrittr_2.0.5
#> [5] TH.data_1.1-5 magick_2.9.1
#> [7] rmarkdown_2.32 vctrs_0.7.3
#> [9] spdep_1.4-2 memoise_2.0.1
#> [11] DelayedMatrixStats_1.35.0 RCurl_1.98-1.20
#> [13] terra_1.9-50 htmltools_0.5.9
#> [15] S4Arrays_1.13.2 BiocBaseUtils_1.15.1
#> [17] AnnotationHub_4.3.2 curl_8.0.0
#> [19] BiocNeighbors_2.7.3 Rhdf5lib_2.1.0
#> [21] s2_1.1.13 LearnBayes_2.15.2
#> [23] SparseArray_1.13.4 rhdf5_2.57.20
#> [25] sass_0.4.10 spData_2.3.5
#> [27] KernSmooth_2.23-27 bslib_0.12.0
#> [29] htmlwidgets_1.6.4 sandwich_3.1-3
#> [31] httr2_1.3.0 zoo_1.9-1
#> [33] cachem_1.1.0 buildtools_1.0.0
#> [35] lifecycle_1.0.5 pkgconfig_2.0.3
#> [37] Matrix_1.7-6 R6_2.6.1
#> [39] fastmap_1.2.0 MatrixGenerics_1.25.0
#> [41] digest_0.6.39 AnnotationDbi_1.75.2
#> [43] S4Vectors_0.51.10 dqrng_0.4.1
#> [45] ExperimentHub_3.3.2 GenomicRanges_1.65.4
#> [47] RSQLite_3.53.3 beachmat_2.29.3
#> [49] filelock_1.0.3 spatialreg_1.4-3
#> [51] httr_1.4.9 abind_1.4-8
#> [53] compiler_4.6.1 proxy_0.4-29
#> [55] bit64_4.8.6 withr_3.0.3
#> [57] backports_1.5.1 tiff_0.1-12
#> [59] BiocParallel_1.47.0 DBI_1.3.0
#> [61] HDF5Array_1.41.3 R.utils_2.13.0
#> [63] MASS_7.3-66 rappdirs_0.3.4
#> [65] DelayedArray_0.39.8 rjson_0.2.23
#> [67] classInt_0.4-11 tools_4.6.1
#> [69] units_1.0-1 otel_0.2.0
#> [71] R.oo_1.27.1 glue_1.8.1
#> [73] h5mread_1.5.3 nlme_3.1-171
#> [75] EBImage_4.55.2 rhdf5filters_1.25.4
#> [77] grid_4.6.1 sf_1.1-3
#> [79] generics_0.1.4 R.methodsS3_1.8.2
#> [81] class_7.3-24 data.table_1.18.6.1
#> [83] sp_2.2-3 XVector_0.53.0
#> [85] BiocGenerics_0.59.12 BiocVersion_3.24.0
#> [87] pillar_1.11.1 limma_3.99.0
#> [89] splines_4.6.1 dplyr_1.2.1
#> [91] BiocFileCache_3.3.0 lattice_0.23-1
#> [93] survival_3.8-12 bit_4.6.0
#> [95] deldir_2.0-4 tidyselect_1.2.1
#> [97] SingleCellExperiment_1.35.2 locfit_1.5-9.12
#> [99] maketools_1.3.2 Biostrings_2.81.9
#> [101] scuttle_1.23.2 sfheaders_0.4.5
#> [103] knitr_1.52 IRanges_2.47.5
#> [105] Seqinfo_1.3.2 edgeR_4.99.6
#> [107] SummarizedExperiment_1.43.0 stats4_4.6.1
#> [109] xfun_0.61 Biobase_2.73.2
#> [111] statmod_1.5.2 DropletUtils_1.33.2
#> [113] matrixStats_1.5.0 fftwtools_0.9-11
#> [115] yaml_2.3.12 boot_1.3-32
#> [117] evaluate_1.0.5 codetools_0.2-20
#> [119] tibble_3.3.1 BiocManager_1.30.27
#> [121] cli_3.6.6 jquerylib_0.1.4
#> [123] Rcpp_1.1.2 zeallot_0.2.0
#> [125] dbplyr_2.6.0 coda_0.19-4.1
#> [127] png_0.1-9 parallel_4.6.1
#> [129] blob_1.3.0 jpeg_0.1-11
#> [131] marginaleffects_1.0.0 sparseMatrixStats_1.25.0
#> [133] bitops_1.1-0 SpatialExperiment_1.23.0
#> [135] mvtnorm_1.4-2 e1071_1.7-17
#> [137] purrr_1.2.2 crayon_1.5.3
#> [139] rlang_1.3.0 multcomp_1.4-32
#> [141] KEGGREST_1.53.6