recipe bioconductor-airpart

Differential cell-type-specific allelic imbalance

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-airpart/meta.yaml

Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.

package bioconductor-airpart

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-apeglm:

>=1.24.0,<1.25.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-scater:

>=1.30.0,<1.31.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-clue:

depends r-dplyr:

depends r-dynamictreecut:

depends r-emdbook:

depends r-forestplot:

depends r-ggplot2:

depends r-lpsolve:

depends r-matrixstats:

depends r-mclust:

depends r-pbapply:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rlang:

depends r-smurf:

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-airpart

and update with::

   mamba update bioconductor-airpart

To create a new environment, run:

mamba create --name myenvname bioconductor-airpart

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-airpart:<tag>

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

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