recipe bioconductor-spaniel

Spatial Transcriptomics Analysis

Homepage

https://bioconductor.org/packages/3.14/bioc/html/Spaniel.html

License

MIT + file LICENSE

Recipe

/bioconductor-spaniel/meta.yaml

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.

package bioconductor-spaniel

Versions

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-dropletutils >=1.14.0,<1.15.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-scater >=1.22.0,<1.23.0

• bioconductor-scran >=1.22.0,<1.23.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-dplyr

• r-ggplot2

• r-igraph

• r-jpeg

• r-jsonlite

• r-magrittr

• r-png

• r-seurat

• r-shiny

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-spaniel

and update with:

conda update bioconductor-spaniel

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-spaniel:<tag>

(see bioconductor-spaniel/tags for valid values for <tag>)

Download stats

Link to this page

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