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>
Repository: https://kharchenkolab.r-universe.dev
Date/Publication: 2022-04-14 14:35:05 UTC
RemoteUrl: https://github.com/kharchenkolab/vrnmf
RemoteRef: HEAD
RemoteSha: 968a29eddad04b92cee7b8067b504082b31d53f8
NeedsCompilation: no
Packaged: 2026-06-21 09:18:42 UTC; root