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 ucdavis.edu>

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

Installation

To install this package, start R (version "3.6") 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")
Gene Detection Analysis for scRNA-seq HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, BatchEffect, DimensionReduction, GeneExpression, KEGG, QualityControl, SingleCell, Software, Transcriptomics
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.6)
Imports SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods
System Requirements
URL https://github.com/ucdavis/quon-titative-biology/BFA
Bug Reports https://github.com/ucdavis/quon-titative-biology/BFA/issues
See More
Suggests knitr, rmarkdown, testthat, Rtsne
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scBFA_1.0.0.tar.gz
Windows Binary scBFA_1.0.0.zip
Mac OS X 10.11 (El Capitan) scBFA_1.0.0.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
Old Source Packages for BioC 3.10 Source Archive