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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "CellProgramMapper" in publications use:'
type: software
license: MIT
title: 'CellProgramMapper: Map Single Cells to Reference Gene Expression Programs'
version: 1.0.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.CellProgramMapper
abstract: 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.
authors:
- family-names: Liu
  given-names: Zaoqu
  email: liuzaoqu@163.com
  orcid: https://orcid.org/0000-0002-0452-742X
preferred-citation:
  type: manual
  title: 'CellProgramMapper: Map Single Cells to Reference Gene Expression Programs'
  authors:
  - family-names: Liu
    given-names: Zaoqu
    email: liuzaoqu@163.com
    orcid: https://orcid.org/0000-0002-0452-742X
  year: '2026'
  notes: R package version 1.0.0
  url: https://github.com/Zaoqu-Liu/CellProgramMapper
repository: https://zaoqu-liu.r-universe.dev
repository-code: https://github.com/Zaoqu-Liu/CellProgramMapper
commit: aa7f0ba8d09dcdb7958f65f4fd9c35cbdd4fcd44
url: https://zaoqu-liu.github.io/CellProgramMapper/
date-released: '2026-01-26'
contact:
- family-names: Liu
  given-names: Zaoqu
  email: liuzaoqu@163.com
  orcid: https://orcid.org/0000-0002-0452-742X
references:
- type: article
  title: Reproducible single-cell annotation of programs underlying T cell subsets,
    activation states and functions
  authors:
  - family-names: Kotliar
    given-names: Dylan
  - name: et al.
  journal: Nature Methods
  year: '2025'
  doi: 10.1038/s41592-025-02793-1