recipe bioconductor-concordexr

Identify Spatial Homogeneous Regions with concordex

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-concordexr/meta.yaml

Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.

package bioconductor-concordexr

versions:

1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biocneighbors:

>=2.0.0,<2.1.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-bluster:

>=1.16.0,<1.17.0

depends bioconductor-delayedarray:

>=0.32.0,<0.33.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

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-cli:

depends r-matrix:

depends r-purrr:

depends r-rlang:

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-concordexr

and update with::

   mamba update bioconductor-concordexr

To create a new environment, run:

mamba create --name myenvname bioconductor-concordexr

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-concordexr:<tag>

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

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