:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-zinbwave' .. highlight: bash bioconductor-zinbwave ===================== .. conda:recipe:: bioconductor-zinbwave :replaces_section_title: :noindex: 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: :biotools:`zinbwave`, doi: :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. .. conda:package:: bioconductor-zinbwave |downloads_bioconductor-zinbwave| |docker_bioconductor-zinbwave| :versions: .. raw:: html
1.24.0-01.22.0-01.20.0-01.16.0-01.14.1-01.12.0-11.12.0-01.10.0-01.8.0-0 ``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`` .. raw:: html
: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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-zinbwave/tags`_ for valid values for ````) .. |downloads_bioconductor-zinbwave| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-zinbwave.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-zinbwave :alt: (downloads) .. |docker_bioconductor-zinbwave| image:: https://quay.io/repository/biocontainers/bioconductor-zinbwave/status :target: https://quay.io/repository/biocontainers/bioconductor-zinbwave .. _`bioconductor-zinbwave/tags`: https://quay.io/repository/biocontainers/bioconductor-zinbwave?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-zinbwave/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-zinbwave/README.html