Package: BUSseq
Type: Package
Title: Batch Effect Correction with Unknow Subtypes for scRNA-seq data
Version: 1.16.0
Date: 2025-10-14
Description: BUSseq R package fits an interpretable Bayesian
        hierarchical model---the Batch Effects Correction with Unknown
        Subtypes for scRNA seq Data (BUSseq)---to correct batch effects
        in the presence of unknown cell types. BUSseq is able to
        simultaneously correct batch effects, clusters cell types, and
        takes care of the count data nature, the overdispersion, the
        dropout events, and the cell-specific sequencing depth of
        scRNA-seq data. After correcting the batch effects with BUSseq,
        the corrected value can be used for downstream analysis as if
        all cells were sequenced in a single batch. BUSseq can
        integrate read count matrices obtained from different scRNA-seq
        platforms and allow cell types to be measured in some but not
        all of the batches as long as the experimental design fulfills
        the conditions listed in our manuscript.
Authors@R: c(person(given = "Fangda", family = "Song", role = c("aut","cre"), email = "sfd1994895@gmail.com", comment = c(ORCID = "0000-0001-6007-3517")), person("Ga Ming", "Chan", role = c("aut"), email = "middletotheleft@gmail.com"), person("Yingying", "Wei", role = c("aut"), email = "ywei@cuhk.edu.hk", comment = c(ORCID = "0000-0003-3826-336X")))
Depends: R (>= 3.6)
License: Artistic-2.0
Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
        grDevices, methods, stats, utils
Suggests: BiocStyle, knitr, BiocGenerics
LazyData: true
Keywords: Single-cell RNA-seq experiments; Batch effects; Model-based
        clustering; Integrative analysis
VignetteBuilder: knitr
biocViews: ExperimentalDesign, GeneExpression, StatisticalMethod,
        Bayesian, Clustering, FeatureExtraction, BatchEffect,
        SingleCell, Sequencing
URL: https://github.com/songfd2018/BUSseq
BugReports: https://github.com/songfd2018/BUSseq/issues
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:10:22 UTC
RemoteUrl: https://github.com/bioc/BUSseq
RemoteRef: RELEASE_3_22
RemoteSha: 95429aa074a3eca02e7b3c515f8aefe8ba813b41
NeedsCompilation: yes
Packaged: 2025-11-11 13:30:06 UTC; root
Author: Fangda Song [aut, cre] (ORCID: <https://orcid.org/0000-0001-6007-3517>),
  Ga Ming Chan [aut],
  Yingying Wei [aut] (ORCID: <https://orcid.org/0000-0003-3826-336X>)
Maintainer: Fangda Song <sfd1994895@gmail.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 13:34:18 UTC; windows
Archs: x64
