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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


Bioconductor version: Development (3.19)

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 "4.4") 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.

Documentation

Reference Manual PDF

Details

biocViews ATACSeq, BatchEffect, DimensionReduction, GeneExpression, KEGG, QualityControl, SingleCell, Software, Transcriptomics
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3 + file LICENSE
Depends R (>= 3.6)
Imports SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix
System Requirements
URL https://github.com/ucdavis/quon-titative-biology/BFA
Bug Reports https://github.com/ucdavis/quon-titative-biology/BFA/issues
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Suggests knitr, rmarkdown, testthat, Rtsne
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64) scBFA_1.17.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/scBFA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scBFA
Bioc Package Browser https://code.bioconductor.org/browse/scBFA/
Package Short Url https://bioconductor.org/packages/scBFA/
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