Package: CellProgramMapper
Type: Package
Title: Map Single Cells to Reference Gene Expression Programs
Version: 1.0.0
Date: 2026-01-26
Authors@R: c(
    person("Zaoqu", "Liu", email = "liuzaoqu@163.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0452-742X"))
    )
Description: Maps single-cell RNA sequencing data to reference gene
        expression programs (GEPs) using non-negative matrix
        factorization. Enables cell type annotation and state
        characterization by projecting query cells onto pre-built or
        custom reference programs. Includes tools for building
        consensus references from multiple datasets. Features C++
        accelerated NNLS solvers and built-in machine learning models
        for cell type prediction.
License: MIT + file LICENSE
URL: https://github.com/Zaoqu-Liu/CellProgramMapper,
        https://zaoqu-liu.github.io/CellProgramMapper/
BugReports: https://github.com/Zaoqu-Liu/CellProgramMapper/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.0), Matrix, methods, stats, utils, curl, yaml,
        future, future.apply, data.table, rappdirs, tools, jsonlite
Suggests: Seurat (>= 4.0.0), SeuratObject (>= 4.0.0), testthat (>=
        3.0.0), knitr, rmarkdown, ggplot2, pheatmap, reshape2, anndata,
        hdf5r, reticulate
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: yes
Config/pak/sysreqs: libssl-dev
Repository: https://zaoqu-liu.r-universe.dev
Date/Publication: 2026-01-26 05:56:10 UTC
RemoteUrl: https://github.com/Zaoqu-Liu/CellProgramMapper
RemoteRef: main
RemoteSha: aa7f0ba8d09dcdb7958f65f4fd9c35cbdd4fcd44
Packaged: 2026-07-03 12:37:50 UTC; root
Author: Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0452-742X>)
Maintainer: Zaoqu Liu <liuzaoqu@163.com>