recipe bioconductor-voyager

From geospatial to spatial omics

Homepage:

https://bioconductor.org/packages/3.18/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:

1.4.0-0,  1.2.3-0,  1.0.3-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-bluster:

>=1.12.0,<1.13.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-spatialexperiment:

>=1.12.0,<1.13.0

depends bioconductor-spatialfeatureexperiment:

>=1.4.0,<1.5.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggnewscale:

depends r-ggplot2:

>=3.4.0

depends r-lifecycle:

depends r-matrix:

depends r-matrixstats:

depends r-patchwork:

depends r-rlang:

depends r-rspectra:

depends r-scales:

depends r-scico:

depends r-sf:

depends r-spdep:

depends r-terra:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-voyager

and update with::

   mamba update bioconductor-voyager

To create a new environment, run:

mamba create --name myenvname bioconductor-voyager

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-voyager/tags`_ for valid values for ``<tag>``)

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