scBFA

This is the development version of scBFA; for the stable release version, see scBFA.

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

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DOI: 10.18129/B9.bioc.scBFA

Bioconductor version: Development (3.23)

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.

Author: Ruoxin Li [aut, cre], Gerald Quon [aut]

Maintainer: Ruoxin Li <uskli at ucdavis.edu>

Citation (from within R, enter citation("scBFA")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scBFA")

For older versions of R, please refer to the appropriate Bioconductor release.