Spaniel

DOI: 10.18129/B9.bioc.Spaniel  

Spatial Transcriptomics Analysis

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Spaniel 10X Visium
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	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 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
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_1.12.0.tar.gz
Windows Binary	Spaniel_1.12.0.zip
macOS Binary (x86_64)	Spaniel_1.12.0.tgz
macOS Binary (arm64)	Spaniel_1.12.0.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