Package: vrnmf
Title: Volume-Regularized Structured Matrix Factorization
Version: 1.0.2
Authors@R: c(person("Ruslan", "Soldatov", email = "ruslansoldatov@gmail.com", role = c("aut")), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"), person("Viktor", "Petukhov", email = "viktor.s.petukhov@ya.ru", role = c("aut")), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role=c("cre", "aut")))
Description: Implements a set of routines to perform structured matrix factorization with minimum volume constraints. The NMF procedure decomposes a matrix X into a product C * D. Given conditions such that the matrix C is non-negative and has sufficiently spread columns, then volume minimization of a matrix D delivers a correct and unique, up to a scale and permutation, solution (C, D). This package provides both an implementation of volume-regularized NMF and "anchor-free" NMF, whereby the standard NMF problem is reformulated in the covariance domain. This algorithm was applied in Vladimir B. Seplyarskiy Ruslan A. Soldatov, et al. "Population sequencing data reveal a compendium of mutational processes in the human germ line". Science, 12 Aug 2021. <doi:10.1126/science.aba7408>. This package interacts with data available through the 'simulatedNMF' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/vrnmf>. The size of the 'simulatedNMF' package is approximately 8 MB.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.1)
Imports: graphics, ica (>= 1.0), lpSolveAPI (>= 5.5.2.0), Matrix, nnls,
        parallel (>= 3.5.1), quadprog (>= 1.5), stats
Suggests: knitr (>= 1.28), rmarkdown (>= 2.1), testthat
RoxygenNote: 7.1.2
URL: https://github.com/kharchenkolab/vrnmf
BugReports: https://github.com/kharchenkolab/vrnmf/issues
Author: Ruslan Soldatov [aut],
  Peter Kharchenko [aut],
  Viktor Petukhov [aut],
  Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
NeedsCompilation: no
Packaged: 2022-02-25 04:13:35 UTC; evanbiederstedt
Repository: CRAN
Date/Publication: 2022-02-25 04:20:02 UTC
Built: R 4.3.3; ; 2025-01-24 13:42:01 UTC; unix
