Package: CellMentor
Type: Package
Title: Supervised Non-negative Matrix Factorization for Dimensional
        Reduction in Single-Cell Analysis
Version: 1.0.1
Authors@R: person("Ekaterina", "Petrenko", 
    email = "petrenko.kate@icloud.com", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-3549-834X"))
Description: Implements supervised cell type-aware non-negative matrix
        factorization (NMF) for dimensional reduction in single-cell
        RNA sequencing analysis. The package provides methods for
        incorporating cell type information into the dimensionality
        reduction process, enabling improved visualization and
        downstream analysis of single-cell data while preserving
        biological structure. CellMentor employs a unique loss function
        that simultaneously minimizes variation within known cell
        populations while maximizing distinctions between different
        cell types, enabling effective transfer of learned patterns
        from labeled reference datasets to new unlabeled data.
License: Apache License (>= 2)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.5.0)
Imports: methods, Matrix, BiocParallel, SingleR, Seurat (>= 4.0.0),
        utils, stats, parallel, progress, ggplot2, data.table,
        magrittr, graphics, RMTstat, sparsesvd, cluster, skmeans,
        MLmetrics, tibble, lsa, nnls, SingleCellExperiment, entropy,
        irlba, aricode
Suggests: testthat (>= 3.0.0), covr, withr, rmarkdown, knitr,
        BiocStyle, scater, scRNAseq
VignetteBuilder: knitr
biocViews: Software, SingleCell, Transcriptomics, DimensionReduction
URL: https://github.com/petrenkokate/CellMentor
BugReports: https://github.com/petrenkokate/CellMentor/issues
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-05-25 16:23:09 UTC
RemoteUrl: https://github.com/bioc/CellMentor
RemoteRef: RELEASE_3_23
RemoteSha: a2a13e2bd5b55274c16ce0806ebfaae56d9c94db
NeedsCompilation: no
Packaged: 2026-10-01 12:01:39 UTC; root
Author: Ekaterina Petrenko [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3549-834X>)
Maintainer: Ekaterina Petrenko <petrenko.kate@icloud.com>