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scBFA

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10

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

DOI: 10.18129/B9.bioc.scBFA

Bioconductor version: Development (3.24)

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")):

Ruoxin Li, Gerald Quon. scBFA: A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq. doi:10.18129/B9.bioc.scBFA, R package version 1.27.0, https://bioconductor.org/packages/scBFA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("scBFA")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scBFA")

Details

Package Archives

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