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Provides functions for the flexible integration of heterogeneous scRNA-seq datasets across multiple tissue types, platforms, and experimental batches. Implements the method described in Ming (2022) <doi:10.1093/bib/bbac167>. The package incorporates modified 'C++' source code from the 'flashpca' library (Abraham, 2014-2016 <https://github.com/gabraham/flashpca>) for efficient principal component analysis, and the 'Spectra' library (Qiu, 2016-2025) for large-scale eigenvalue and singular value decomposition; see 'inst/COPYRIGHTS' for details on third-party code.
| Version: | 0.1.2 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Seurat (≥ 5.0.0), RANN |
| LinkingTo: | Rcpp, RcppArmadillo, RcppEigen |
| Suggests: | ggplot2 |
| Published: | 2026-02-19 |
| DOI: | 10.32614/CRAN.package.FIRM |
| Author: | Jingsi Ming [aut, cre, cph] (R package development and method implementation, ORCID: 0000-0001-7059-4156), Shuzhen Ding [ctb] (R package development and maintenance), Gad Abraham [ctb, cph] (Original 'flashpca' 'C++' code for fast randomized PCA), Yixuan Qiu [ctb, cph] ('Spectra' library for large-scale eigenvalue and SVD computation), Anna Araslanova [ctb, cph] (Author of 'LOBPCGSolver.h' in 'Spectra'), Felipe Zapata [ctb, cph] (Author of 'DavidsonSymEigsSolver.h' and 'Orthogonalization.h' in 'Spectra' (Netherlands eScience Center)), Nicolas Renaud [ctb, cph] (Author of 'RitzPairs.h' and 'SearchSpace.h' in 'Spectra' (Netherlands eScience Center)), Jens Wehner [ctb, cph] (Author of 'JDSymEigsBase.h' in 'Spectra' (Netherlands eScience Center)), Gael Guennebaud [ctb, cph] ('Eigen' library code for tridiagonal eigenvalue decomposition), Jitse Niesen [ctb, cph] ('Eigen' library code for eigenvalue computation) |
| Maintainer: | Jingsi Ming <jsming at fem.ecnu.edu.cn> |
| BugReports: | https://github.com/mingjingsi/FIRM/issues |
| License: | GPL-3 |
| Copyright: | See file 'inst/COPYRIGHTS' for details. FIRM copyright details |
| URL: | https://github.com/mingjingsi/FIRM |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | FIRM results |
| Reference manual: | FIRM.html , FIRM.pdf |
| Package source: | FIRM_0.1.2.tar.gz |
| Windows binaries: | r-devel: not available, r-release: FIRM_0.1.2.zip, r-oldrel: FIRM_0.1.2.zip |
| macOS binaries: | r-release (arm64): FIRM_0.1.2.tgz, r-oldrel (arm64): FIRM_0.1.2.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.