Spaniel
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Spaniel.
Spatial Transcriptomics Analysis
Bioconductor version: 3.10
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("Spaniel")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, Coverage, DataImport, DataRepresentation, GeneExpression, Infrastructure, Normalization, Preprocessing, QualityControl, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.0.0 |
| 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_1.0.0.tar.gz |
| Windows Binary | Spaniel_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | Spaniel_1.0.0.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 3.10 | Source Archive |