recipe bioconductor-scbfa

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

Homepage

https://bioconductor.org/packages/3.12/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

1.4.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-deseq2 >=1.30.0,<1.31.0

• bioconductor-singlecellexperiment >=1.12.0,<1.13.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• bioconductor-zinbwave >=1.12.0,<1.13.0

• r-base >=4.0,<4.1.0a0

• 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>)

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-scbfa/README.html)