Package: scBFA
Version: 1.1.0
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
Suggests: knitr, rmarkdown, testthat, Rtsne
VignetteBuilder: knitr
RoxygenNote: 6.1.1
License: GPL-3
LazyData: true
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/scBFA
git_branch: master
git_last_commit: 5790338
git_last_commit_date: 2019-10-29
Date/Publication: 2019-12-16
NeedsCompilation: no
Packaged: 2019-12-17 06:21:44 UTC; biocbuild
Author: Ruoxin Li [aut, cre],
  Gerald Quon [aut]
Maintainer: Ruoxin Li <uskli@ucdavis.edu>
Built: R 4.0.0; ; 2019-12-17 15:27:47 UTC; unix
