Package Recipe 'bioconductor-lisaclust'

recipe bioconductor-lisaclust

lisaClust: Clustering of Local Indicators of Spatial Association

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/lisaClust.html
License:: GPL (>=2)
Recipe:: /bioconductor-lisaclust/meta.yaml

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

package bioconductor-lisaclust¶

Versions:

1.18.0-0, 1.14.0-0, 1.10.1-0, 1.8.0-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-simpleseg >=1.12.0,<1.13.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on bioconductor-spicyr >=1.22.0,<1.23.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-class
on r-concaveman
on r-data.table
on r-dplyr
on r-ggplot2
on r-lifecycle
on r-pheatmap
on r-purrr
on r-rlang
on r-spatstat.explore
on r-spatstat.geom
on r-spatstat.random
on r-tidyr

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-lisaclust

to add into an existing workspace instead, run:

pixi add bioconductor-lisaclust

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-lisaclust

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-lisaclust

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-lisaclust:<tag>

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