Package: scBFA
Version: 1.24.0
Date: 2019-03-09
Title: A dimensionality reduction tool using gene detection pattern to
        mitigate noisy expression profile of scRNA-seq
Description: 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.
Authors@R: 
   c(person(given = "Ruoxin",
            family = "Li",
            role = c("aut", "cre"),
            email = "uskli@ucdavis.edu"),
     person(given = "Gerald",
            family = "Quon",
            role = c("aut"),
            email = "gquon@ucdavis.edu"))
URL: https://github.com/ucdavis/quon-titative-biology/BFA
BugReports: https://github.com/ucdavis/quon-titative-biology/BFA/issues
biocViews: SingleCell, Transcriptomics,
        DimensionReduction,GeneExpression, ATACSeq, BatchEffect, KEGG,
        QualityControl
Depends: R (>= 3.6)
Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS,
        zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods,
        Matrix
Suggests: knitr, rmarkdown, testthat, Rtsne
VignetteBuilder: knitr
RoxygenNote: 7.0.2
License: GPL-3 + file LICENSE
LazyData: true
Encoding: UTF-8
Config/pak/sysreqs: libglpk-dev make libgsl0-dev libicu-dev libpng-dev
        libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:53:24 UTC
RemoteUrl: https://github.com/bioc/scBFA
RemoteRef: RELEASE_3_22
RemoteSha: f8bf5ba44174d700d256c503b20759971f0262c8
NeedsCompilation: no
Packaged: 2026-03-13 08:00:48 UTC; root
Author: Ruoxin Li [aut, cre],
  Gerald Quon [aut]
Maintainer: Ruoxin Li <uskli@ucdavis.edu>
Built: R 4.5.3; ; 2026-03-13 08:04:33 UTC; windows
