scBFA

DOI: 10.18129/B9.bioc.scBFA  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	Gene Detection Analysis for scRNA-seq
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, BatchEffect, DimensionReduction, GeneExpression, KEGG, QualityControl, SingleCell, Software, Transcriptomics
Version	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.6)
Imports	SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix
LinkingTo
Suggests	knitr, rmarkdown, testthat, Rtsne
SystemRequirements
Enhances
URL	https://github.com/ucdavis/quon-titative-biology/BFA
BugReports	https://github.com/ucdavis/quon-titative-biology/BFA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scBFA_1.12.0.tar.gz
Windows Binary	scBFA_1.12.0.zip
macOS Binary (x86_64)	scBFA_1.12.0.tgz
macOS Binary (arm64)	scBFA_1.12.0.tgz
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/
Package Downloads Report	Download Stats