Spaniel

DOI: 10.18129/B9.bioc.Spaniel    

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

Spatial Transcriptomics Analysis

Bioconductor version: Development (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 (!requireNamespace("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")

 

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 1.1.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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_1.1.0.tar.gz
Windows Binary Spaniel_1.1.0.zip
Mac OS X 10.11 (El Capitan) Spaniel_1.1.0.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

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