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 (3.24)
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("scBFA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| Gene Detection Analysis for scRNA-seq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ATACSeq, BatchEffect, DimensionReduction, GeneExpression, KEGG, QualityControl, SingleCell, Software, Transcriptomics |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 |
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_1.27.0.tar.gz |
| Windows Binary (x86_64) | scBFA_1.27.0.zip |
| macOS Binary (big-sur-x86_64) | scBFA_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | scBFA_1.27.0.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 |