SubcellularSpatialData | Download data from the SubcellularSpatialData R package | Summarising transcripts into cells, bins, and regions | Session Info
Package: SubcellularSpatialData 1.8.0
Dharmesh D. Bhuva
SubcellularSpatialData: Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics.
This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented.
Authors:
SubcellularSpatialData_1.8.0.tar.gz
SubcellularSpatialData_1.8.0.tar.gz(r-4.7-any)SubcellularSpatialData_1.8.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SubcellularSpatialData/json (API)
| # Install 'SubcellularSpatialData' in R: |
| install.packages('SubcellularSpatialData', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davislaboratory/subcellularspatialdata/issues
Datasets:
- tx_small - Sample annotated sub-cellular localised spatial 'omics dataset
On BioConductor:SubcellularSpatialData-1.9.0(data/experiment 3.24)SubcellularSpatialData-1.8.0(data/experiment 3.23)
experimenthubspatialdatahomo_sapiens_datamus_musculus_datalungcancerdatadatapkg
Last updated from:7ec55d259b (on RELEASE_3_23). Checks:3 NOTE, 1 OK. Indexed: no.
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 | NOTE | 156 | ||
| linux-devel | NOTE | 206 | ||
| source / vignettes | OK | 278 | ||
| linux-release | NOTE | 232 |
Exports:tx2spe
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11curlDBIdbplyrDelayedArraydplyrfastmapfilelockgenericsGenomicRangesgluehexbinhttr2IRangeslatticelifecyclemagickmagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6RcpprjsonrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySpatialExperimentstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVector
