Spaniel

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see Spaniel.

Spatial Transcriptomics Analysis


Bioconductor version: 3.11

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>

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

Installation

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


if (!require("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")
Using Spaniel HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, Coverage, DataImport, DataRepresentation, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.2.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements
URL
See More
Suggests knitr, rmarkdown, testthat, devtools
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package Spaniel_1.2.0.tar.gz
Windows Binary Spaniel_1.2.0.zip
macOS 10.13 (High Sierra) Spaniel_1.2.0.tgz
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
Old Source Packages for BioC 3.11 Source Archive