recipe bioconductor-singlecellalleleexperiment

S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-singlecellalleleexperiment/meta.yaml

Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.

package bioconductor-singlecellalleleexperiment

versions:

1.2.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-delayedarray:

>=0.32.0,<0.33.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

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-singlecellalleleexperiment

and update with::

   mamba update bioconductor-singlecellalleleexperiment

To create a new environment, run:

mamba create --name myenvname bioconductor-singlecellalleleexperiment

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-singlecellalleleexperiment:<tag>

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

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