recipe bioconductor-scbfa

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

Homepage

https://bioconductor.org/packages/3.14/bioc/html/scBFA.html

License

GPL-3 + file LICENSE

Recipe

/bioconductor-scbfa/meta.yaml

This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis.

package bioconductor-scbfa

Versions

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-deseq2 >=1.34.0,<1.35.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-zinbwave >=1.16.0,<1.17.0

• r-base >=4.1,<4.2.0a0

• r-copula

• r-ggplot2

• r-mass

• r-matrix

• r-seurat

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-scbfa

and update with:

conda update bioconductor-scbfa

or use the docker container:

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

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

Download stats

Link to this page

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