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Spaniel

This is the development version of Spaniel; for the stable release version, see Spaniel.

Spatial Transcriptomics Analysis


Bioconductor version: Development (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 newcastle.ac.uk>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("Spaniel")

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

Documentation

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

browseVignettes("Spaniel")
Spaniel 10X Visium HTML R Script
Reference Manual PDF

Details

biocViews Clustering, Coverage, DataImport, DataRepresentation, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.17.0
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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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package Spaniel_1.17.0.tar.gz
Windows Binary
macOS Binary (x86_64) Spaniel_1.17.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/Spaniel
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Spaniel
Bioc Package Browser https://code.bioconductor.org/browse/Spaniel/
Package Short Url https://bioconductor.org/packages/Spaniel/
Package Downloads Report Download Stats