Package Recipe 'bioconductor-voyager'

recipe bioconductor-voyager

From geospatial to spatial omics

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

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The Voyager package also implements plotting functions to plot SFE data and ESDA results.

package bioconductor-voyager¶

Versions:

1.12.0-0, 1.8.1-0, 1.4.0-0, 1.2.3-0, 1.0.3-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-bluster >=1.20.0,<1.21.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
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-spatialfeatureexperiment >=1.12.0,<1.13.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-ggnewscale
on r-ggplot2 >=3.4.0
on r-lifecycle
on r-matrix
on r-memuse
on r-patchwork
on r-rlang
on r-rspectra
on r-scales
on r-scico
on r-sf
on r-spdep
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-voyager

to add into an existing workspace instead, run:

pixi add bioconductor-voyager

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-voyager

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-voyager

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-voyager:<tag>

(see bioconductor-voyager/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-voyager/README.html)