recipe bioconductor-zinbwave

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Homepage:

https://bioconductor.org/packages/3.16/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:

1.20.0-0,  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, 

1.20.0-0,  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 >=1.32.0,<1.33.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-genefilter >=1.80.0,<1.81.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-matrix

• r-softimpute

Required By:

• bioconductor-singlecelltk

• bioconductor-benchdamic

• bioconductor-clusterexperiment

• bioconductor-scbfa

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-zinbwave

and update with:

conda update bioconductor-zinbwave

or 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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