recipe bioconductor-newwave

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.

package 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:

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-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:<tag>

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

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