Package: CellMentor
Type: Package
Title: Supervised Non-negative Matrix Factorization for Dimensional
        Reduction in Single-Cell Analysis
Version: 0.99.0
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 (>= 4.3.0)
Imports: methods, Matrix, SingleR, Seurat (>= 4.0.0), utils, stats,
        parallel, progress, ggplot2, data.table, magrittr, graphics,
        RMTstat, sparsesvd, cluster, skmeans, MLmetrics, tibble, lsa,
        nnls, scRNAseq, SingleCellExperiment, entropy, irlba, aricode
Suggests: testthat (>= 3.0.0), covr, withr, rmarkdown, knitr,
        BiocStyle, scater
VignetteBuilder: knitr
biocViews: Software, SingleCell, GeneExpression, Transcriptomics,
        DimensionReduction
URL: https://github.com/petrenkokate/CellMentor
BugReports: https://github.com/petrenkokate/CellMentor/issues
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/CellMentor
git_branch: devel
git_last_commit: 7854b85
git_last_commit_date: 2025-11-04
Repository: Bioconductor 3.23
Date/Publication: 2026-01-13
NeedsCompilation: no
Packaged: 2026-01-13 21:52:09 UTC; biocbuild
Author: Ekaterina Petrenko [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3549-834X>)
Maintainer: Ekaterina Petrenko <petrenko.kate@icloud.com>
