Package Recipe 'bioconductor-newwave'

recipe bioconductor-newwave

Negative binomial model for scRNA-seq

Homepage:: https://bioconductor.org/packages/3.20/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:

1.20.0-0, 1.16.0-0, 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:

on bioconductor-biocsingular >=1.26.0,<1.27.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-sharedobject >=1.24.0,<1.25.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-irlba
on r-matrix

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-newwave

to add into an existing workspace instead, run:

pixi add bioconductor-newwave

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-newwave

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-newwave

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-newwave:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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)