recipe bioconductor-zinbwave

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-zinbwave/meta.yaml

Links:

biotools: zinbwave, doi: 10.1038/s41467-017-02554-5

Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.

package bioconductor-zinbwave

versions:

1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.1-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0, 

1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.1-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

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-matrix:

depends r-softimpute:

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-zinbwave

and update with::

   mamba update bioconductor-zinbwave

To create a new environment, run:

mamba create --name myenvname bioconductor-zinbwave

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-zinbwave:<tag>

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

Download stats

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