| Title: | Visium spatial gene expression data by 10X Genomics |
|---|---|
| Description: | Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes. |
| Authors: | Helena L. Crowell [aut, cre] (ORCID: <https://orcid.org/0000-0002-4801-1767>) |
| Maintainer: | Helena L. Crowell <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.20.0 |
| Built: | 2026-10-10 11:15:26 UTC |
| Source: | https://github.com/bioc/TENxVisiumData |
Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes.
The following Visium Spatial Transcriptomics datasets by 10X Genomics are currently available (see the package vignette for links to details):
HumanBreastCancerIDC
HumanBreastCancerILC
HumanCerebellum
HumanColorectalCancer
HumanGlioblastoma
HumanHeart
HumanLymphNode
HumanOvarianCancer
HumanSpinalCord
MouseBrainCoronal
MouseBrainSagittalPosterior
MouseBrainSagittalAnterior
MouseKidneyCoronal
a SpatialExperiment
with rows corresponding to samples (spots)
and columns to features (transcripts).
If, in addition to whole transcriptome analysis,
the specified dataset contains measurements
from targeted panel analysis/es,
these will be stored as altExps.
Helena L. Crowell
# initialize hub instance eh <- ExperimentHub() # query for TENxVisium datasets (q <- query(eh, "TENxVisium")) # retrieve dataset of interest pat <- "HumanCerebellum$" idx <- grep(pat, q$title) id <- q$ah_id[idx] (spe <- eh[[id]]) # access targeted panel altExpNames(spe) altExp(spe, "TargetedNeuroscience")# initialize hub instance eh <- ExperimentHub() # query for TENxVisium datasets (q <- query(eh, "TENxVisium")) # retrieve dataset of interest pat <- "HumanCerebellum$" idx <- grep(pat, q$title) id <- q$ah_id[idx] (spe <- eh[[id]]) # access targeted panel altExpNames(spe) altExp(spe, "TargetedNeuroscience")