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Spatial Transcriptomics Analysis

Bioconductor version: Release (3.19)

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

Author: Rachel Queen [aut, cre]

Maintainer: Rachel Queen <rachel.queen at>

Citation (from within R, enter citation("Spaniel")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Spaniel 10X Visium HTML R Script
Reference Manual PDF


biocViews Clustering, Coverage, DataImport, DataRepresentation, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater(>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png
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Suggests knitr, rmarkdown, testthat, devtools
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Follow Installation instructions to use this package in your R session.

Source Package Spaniel_1.18.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) Spaniel_1.18.0.tgz
macOS Binary (arm64) Spaniel_1.18.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive