recipe bioconductor-asurat

Functional annotation-driven unsupervised clustering for single-cell data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/ASURAT.html

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-asurat/meta.yaml

ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

package bioconductor-asurat

versions:

1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-1,  1.2.0-0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0a0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-cluster:

depends r-plot3d:

depends r-rcpp:

>=1.0.7

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-asurat

and update with::

   mamba update bioconductor-asurat

To create a new environment, run:

mamba create --name myenvname bioconductor-asurat

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-asurat:<tag>

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

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