recipe bioconductor-smoothclust

smoothclust

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/smoothclust.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-smoothclust/meta.yaml

Method for segmentation of spatial domains and spatially-aware clustering in spatial transcriptomics data. The method generates spatial domains with smooth boundaries by smoothing gene expression profiles across neighboring spatial locations, followed by unsupervised clustering. Spatial domains consisting of consistent mixtures of cell types may then be further investigated by applying cell type compositional analyses or differential analyses.

package bioconductor-smoothclust

(downloads) docker_bioconductor-smoothclust

versions:

1.2.0-0

depends bioconductor-sparsematrixstats:

>=1.18.0,<1.19.0

depends bioconductor-spatialexperiment:

>=1.16.0,<1.17.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-spdep:

requirements:

additional platforms:

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-smoothclust

and update with::

   mamba update bioconductor-smoothclust

To create a new environment, run:

mamba create --name myenvname bioconductor-smoothclust

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-smoothclust:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-smoothclust/README.html)