DOI: 10.18129/B9.bioc.scBFA    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see scBFA.

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

Bioconductor version: 3.10

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>

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


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biocViews ATACSeq, BatchEffect, DimensionReduction, GeneExpression, KEGG, QualityControl, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License GPL-3
Depends R (>= 3.6)
Imports SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods
Suggests knitr, rmarkdown, testthat, Rtsne
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Source Package scBFA_1.0.0.tar.gz
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