recipe bioconductor-stabmap

Stabilised mosaic single cell data integration using unshared features

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-stabmap/meta.yaml

StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.

package bioconductor-stabmap

versions:

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-biocsingular:

>=1.22.0,<1.23.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-abind:

depends r-base:

>=4.4,<4.5.0a0

depends r-igraph:

depends r-mass:

depends r-matrix:

depends r-slam:

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-stabmap

and update with::

   mamba update bioconductor-stabmap

To create a new environment, run:

mamba create --name myenvname bioconductor-stabmap

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-stabmap:<tag>

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

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