Spaniel
Spatial Transcriptomics Analysis
Bioconductor version: Release (3.20)
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>
citation("Spaniel")):
Installation
To install this package, start R (version "4.4") 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")| Spaniel 10X Visium | 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 | 1.20.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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 |
| 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_1.20.0.tar.gz |
| Windows Binary (x86_64) | Spaniel_1.20.0.zip |
| macOS Binary (x86_64) | Spaniel_1.20.0.tgz |
| macOS Binary (arm64) | Spaniel_1.20.0.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 |