recipe bioconductor-aucell

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-aucell/meta.yaml

AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules…) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

package bioconductor-aucell

versions:

1.24.0-0,  1.22.0-0,  1.20.1-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

1.24.0-0,  1.22.0-0,  1.20.1-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.1-0,  1.4.1-0,  1.4.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-delayedmatrixstats:

>=1.24.0,<1.25.0

depends bioconductor-gseabase:

>=1.64.0,<1.65.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-matrix:

depends r-mixtools:

depends r-r.utils:

depends r-shiny:

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-aucell

and update with::

   mamba update bioconductor-aucell

To create a new environment, run:

mamba create --name myenvname bioconductor-aucell

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-aucell:<tag>

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

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