Spaniel

DOI: 10.18129/B9.bioc.Spaniel    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Spaniel.

Spatial Transcriptomics Analysis

Bioconductor version: 3.12

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. The package contains functions to create either a Seurat object or SingleCellExperiment from a count matrix and spatial barcode file 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 <rachel.queen at newcastle.ac.uk>

Maintainer: Rachel Queen <rachel.queen at newcastle.ac.uk>

Installation

To install this package, start R (version "4.0") and enter:

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

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")

 

HTML	R Script	Using Spaniel
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, Coverage, DataImport, DataRepresentation, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), Seurat, SingleCellExperiment, SummarizedExperiment, dplyr
Imports	methods, ggplot2, scater(>= 1.13.27), shiny, jpeg, magrittr, utils, S4Vectors
LinkingTo
Suggests	knitr, rmarkdown, testthat, devtools
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Spaniel_1.4.0.tar.gz
Windows Binary	Spaniel_1.4.0.zip
macOS 10.13 (High Sierra)	Spaniel_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Spaniel
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Spaniel
Package Short Url	https://bioconductor.org/packages/Spaniel/
Package Downloads Report	Download Stats