This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see Spaniel.
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 (from within R,
enter citation("Spaniel")
):
To install this package, start R (version "3.6") 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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Spaniel")
HTML | R Script | Using Spaniel |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
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) (< 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 |
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 |
Package Short Url | https://bioconductor.org/packages/Spaniel/ |
Package Downloads Report | Download Stats |
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