Introduction | Installation | Datasets | Load data | Load using named accessors | Visium_humanDLPFC | Visium_mouseCoronal | seqFISH_mouseEmbryo | ST_mouseOB | SlideSeqV2_mouseHPC | Janesick_breastCancer_Chromium | Janesick_breastCancer_Visium | Janesick_breastCancer_Xenium_rep1 | Janesick_breastCancer_Xenium_rep2 | CosMx_lungCancer | MERSCOPE_ovarianCancer | STARmapPLUS_mouseBrain | Load by querying ExperimentHub database | Generating objects from raw data files | Session information
Package: STexampleData 1.21.1
Lukas M. Weber
STexampleData: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format
Collection of spatial transcriptomics datasets stored in SpatialExperiment Bioconductor format, for use in examples, demonstrations, and tutorials. The datasets are from several different platforms and have been sourced from various publicly available sources. Several datasets include images and/or reference annotation labels.
Authors:
STexampleData_1.21.1.tar.gz
STexampleData_1.21.1.tar.gz(r-4.7-any)STexampleData_1.21.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
STexampleData/json (API)
| # Install 'STexampleData' in R: |
| install.packages('STexampleData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lmweber/stexampledata/issues
On BioConductor:STexampleData-1.21.1(data/experiment 3.24)STexampleData-1.20.1(data/experiment 3.23)
experimentdataexperimenthubreproducibleresearchexpressiondatasinglecelldataspatialdatahomo_sapiens_datamus_musculus_datadatapkg
Last updated from:6669806d41. Checks:1 WARNING, 2 NOTE, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 169 | ||
| linux-devel | NOTE | 321 | ||
| source / vignettes | OK | 312 | ||
| linux-release | NOTE | 327 |
Exports:CosMx_lungCancerJanesick_breastCancer_ChromiumJanesick_breastCancer_VisiumJanesick_breastCancer_Xenium_rep1Janesick_breastCancer_Xenium_rep2MERSCOPE_ovarianCancerseqFISH_mouseEmbryoSlideSeqV2_mouseHPCST_mouseOBSTARmapPLUS_mouseBrainVisium_humanDLPFCVisium_mouseCoronal
Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfastmapfilelockgenericsGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsRcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format | STexampleData-package CosMx_lungCancer Janesick_breastCancer_Chromium Janesick_breastCancer_Visium Janesick_breastCancer_Xenium_rep1 Janesick_breastCancer_Xenium_rep2 MERSCOPE_ovarianCancer seqFISH_mouseEmbryo SlideSeqV2_mouseHPC STARmapPLUS_mouseBrain STexampleData ST_mouseOB Visium_humanDLPFC Visium_mouseCoronal |