:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-newwave' .. highlight: bash bioconductor-newwave ==================== .. conda:recipe:: bioconductor-newwave :replaces_section_title: :noindex: Negative binomial model for scRNA\-seq :homepage: https://bioconductor.org/packages/3.18/bioc/html/NewWave.html :license: GPL-3 :recipe: /`bioconductor-newwave `_/`meta.yaml `_ A model designed for dimensionality reduction and batch effect removal for scRNA\-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication\, and it can be used with different mini\-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise. .. conda:package:: bioconductor-newwave |downloads_bioconductor-newwave| |docker_bioconductor-newwave| :versions: ``1.12.0-0``,  ``1.8.0-0``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.2-0``,  ``0.99.10-1`` :depends bioconductor-biocsingular: ``>=1.18.0,<1.19.0`` :depends bioconductor-delayedarray: ``>=0.28.0,<0.29.0`` :depends bioconductor-sharedobject: ``>=1.16.0,<1.17.0`` :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-irlba: :depends r-matrix: :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-newwave and update with:: mamba update bioconductor-newwave To create a new environment, run:: mamba create --name myenvname bioconductor-newwave 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-newwave: (see `bioconductor-newwave/tags`_ for valid values for ````) .. |downloads_bioconductor-newwave| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-newwave.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-newwave :alt: (downloads) .. |docker_bioconductor-newwave| image:: https://quay.io/repository/biocontainers/bioconductor-newwave/status :target: https://quay.io/repository/biocontainers/bioconductor-newwave .. _`bioconductor-newwave/tags`: https://quay.io/repository/biocontainers/bioconductor-newwave?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-newwave/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-newwave/README.html