Package Recipe 'bioconductor-spatialfeatureexperiment'

recipe bioconductor-spatialfeatureexperiment

Integrating SpatialExperiment with Simple Features in sf

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/SpatialFeatureExperiment.html
License:: Artistic-2.0
Recipe:: /bioconductor-spatialfeatureexperiment/meta.yaml

A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.

package bioconductor-spatialfeatureexperiment¶

Versions:

1.12.1-0, 1.8.0-0, 1.4.0-0, 1.2.1-0, 1.0.0-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocneighbors >=2.4.0,<2.5.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-dropletutils >=1.30.0,<1.31.0
on bioconductor-ebimage >=4.52.0,<4.53.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-lifecycle
on r-matrix
on r-rjson
on r-rlang
on r-sf
on r-sfheaders
on r-spatialreg
on r-spdep >=1.1-7
on r-terra
on r-zeallot

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-spatialfeatureexperiment

to add into an existing workspace instead, run:

pixi add bioconductor-spatialfeatureexperiment

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-spatialfeatureexperiment

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-spatialfeatureexperiment

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-spatialfeatureexperiment/README.html)