recipe bioconductor-spatialexperiment

S4 Class for Spatially Resolved Transcriptomics Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/SpatialExperiment.html

License:

GPL-3

Recipe:

/bioconductor-spatialexperiment/meta.yaml

Defines an S4 class for storing data from spatially resolved transcriptomics (ST) experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based ST platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

package bioconductor-spatialexperiment

Versions:

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

Depends:

• bioconductor-biocfilecache >=2.6.0,<2.7.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-dropletutils >=1.18.0,<1.19.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-magick

• r-rjson

Required By:

• bioconductor-lisaclust

• bioconductor-spasim

• bioconductor-spatiallibd

• bioconductor-vectrapolarisdata

• bioconductor-spiat

• bioconductor-imcrtools

• bioconductor-experimentsubset

• bioconductor-cytomapper

• bioconductor-ggspavis

• bioconductor-stexampledata

• bioconductor-tenxvisiumdata

• bioconductor-nnsvg

• bioconductor-merfishdata

• bioconductor-singlecellmultimodal

• bioconductor-weberdivechalcdata

• bioconductor-spatialfeatureexperiment

• bioconductor-stjoincount

• bioconductor-spatialde

• bioconductor-spotclean

• bioconductor-mousegastrulationdata

• bioconductor-ctsv

• bioconductor-imcdatasets

• bioconductor-standr

• bioconductor-spicyr

• bioconductor-voyager

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-spatialexperiment

and update with:

conda update bioconductor-spatialexperiment

or use the docker container:

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

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-spatialexperiment/README.html)