{ "_id": "6ad5d0da4a34890ab4938d2e", "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\nfactorization with minimum volume constraints. The NMF\nprocedure decomposes a matrix X into a product C * D. Given\nconditions such that the matrix C is non-negative and has\nsufficiently spread columns, then volume minimization of a\nmatrix D delivers a correct and unique, up to a scale and\npermutation, solution (C, D). This package provides both an\nimplementation of volume-regularized NMF and \"anchor-free\" NMF,\nwhereby the standard NMF problem is reformulated in the\ncovariance domain. This algorithm was applied in Vladimir B.\nSeplyarskiy Ruslan A. Soldatov, et al. \"Population sequencing\ndata reveal a compendium of mutational processes in the human\ngerm line\". Science, 12 Aug 2021.\n. This package interacts with data\navailable through the 'simulatedNMF' package, which is\navailable in a 'drat' repository. To access this data package,\nsee the instructions at\n. The size of the\n'simulatedNMF' package is approximately 8 MB.", "License": "GPL-3", "Encoding": "UTF-8", "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\n[aut], Evan Biederstedt [cre, aut]", "Maintainer": "Evan Biederstedt ", "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": { "Date": "2026-10-19 08:06:12 UTC", "User": "root" }, "_user": "kharchenkolab", "_type": "src", "_file": "vrnmf_1.0.2.tar.gz", "_fileid": "https://r2.ropensci.org/d9626b74fa1569028cf21ef34ba9a94d1b445d7ec6ec4ef6e1d02c430b482843", "_filesize": 174944, "_sha256": "d9626b74fa1569028cf21ef34ba9a94d1b445d7ec6ec4ef6e1d02c430b482843", "_expires": "2027-01-27T08:12:08.000Z", "_created": "2026-10-19T08:06:12.000Z", "_published": "2026-10-19T08:12:10.251Z", "_buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117954170441, "time": 112, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12171302750" }, { "job": 117954170487, "time": 207, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12171622032" }, { "job": 117954170494, "time": 104, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12170969814" }, { "job": 117954170295, "time": 117, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12171133922" }, { "job": 117951949719, "time": 357, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12171925240" }, { "job": 117954170263, "time": 235, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12171119462" }, { "job": 117954170489, "time": 85, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12170944633" }, { "job": 117954170520, "time": 86, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12171372404" }, { "job": 117954170530, "time": 318, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12170939120" } ], "_upstream": "https://github.com/kharchenkolab/vrnmf", "_commit": { "id": "968a29eddad04b92cee7b8067b504082b31d53f8", "author": "evanbiederstedt ", "committer": "GitHub ", "message": "Update README.md", "time": 1649946905 }, "_maintainer": { "name": "Evan Biederstedt", "email": "evan.biederstedt@gmail.com", "login": "evanbiederstedt", "description": "", "uuid": 6968193 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.1", "role": "Depends" }, { "package": "graphics", "role": "Imports" }, { "package": "ica", "version": ">= 1.0", "role": "Imports" }, { "package": "lpSolveAPI", "version": ">= 5.5.2.0", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "nnls", "role": "Imports" }, { "package": "parallel", "version": ">= 3.5.1", "role": "Imports" }, { "package": "quadprog", "version": ">= 1.5", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "version": ">= 1.28", "role": "Suggests" }, { "package": "rmarkdown", "version": ">= 2.1", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "kharchenkolab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 18, "_contributors": [ { "user": "solrust", "count": 73, "uuid": 29613906 }, { "user": "evanbiederstedt", "count": 39, "uuid": 6968193 }, { "user": "pkharchenko", "count": 1, "uuid": 11860978 } ], "_userbio": { "uuid": 67511277, "type": "organization", "name": "Kharchenko Lab", "followers": 95 }, "_downloads": { "count": 314, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vrnmf" }, "_devurl": "https://github.com/kharchenkolab/vrnmf", "_searchresults": 13, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "extra/vrnmf.html" ], "_homeurl": "https://github.com/kharchenkolab/vrnmf", "_realowner": "kharchenkolab", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-08-20" }, { "version": "1.0.1", "date": "2022-01-14" }, { "version": "1.0.2", "date": "2022-02-25" } ], "_exports": [ "AnchorFree", "factor_intensities", "infer_intensities", "projection_onto_simplex", "sim_factors", "vol_preprocess", "volnmf_det", "volnmf_estimate", "volnmf_logdet", "volnmf_main", "volnmf_procrustes", "volnmf_simplex_col", "volnmf_simplex_row" ], "_help": [ { "page": "AnchorFree", "title": "Non-negative tri-factorization of co-occurence matrix using minimum volume approach.", "topics": [ "AnchorFree" ] }, { "page": "factor_intensities", "title": "Infer a matrix of non-negative intensities in NMF with offset/nmf-offset.", "topics": [ "factor_intensities" ] }, { "page": "infer_intensities", "title": "Infer a matrix of non-negative intensities in NMF", "topics": [ "infer_intensities" ] }, { "page": "projection_onto_simplex", "title": "Project vector onto a probabilistic simplex.", "topics": [ "projection_onto_simplex" ] }, { "page": "sim_factors", "title": "Simulate matrices to explores 'vrnmf'", "topics": [ "sim_factors" ] }, { "page": "vol_preprocess", "title": "Preprocess the data for downstream volume analysis.", "topics": [ "vol_preprocess" ] }, { "page": "volnmf_det", "title": "Update volume-regularized matrix 'R' using det volume approximation", "topics": [ "volnmf_det" ] }, { "page": "volnmf_estimate", "title": "Alternating optimization of volume-regularized NMF", "topics": [ "volnmf_estimate" ] }, { "page": "volnmf_logdet", "title": "Update volume-regularized matrix 'R' using logdet volume approximation.", "topics": [ "volnmf_logdet" ] }, { "page": "volnmf_main", "title": "Volume-regularized NMF", "topics": [ "volnmf_main" ] }, { "page": "volnmf_procrustes", "title": "Procrustes algorithm estimates orthonormal transformation between two matrices.", "topics": [ "volnmf_procrustes" ] }, { "page": "volnmf_simplex_col", "title": "Update of a matrix in NMF with equality contstraints on columns.", "topics": [ "volnmf_simplex_col" ] }, { "page": "volnmf_simplex_row", "title": "Update of a matrix in NMF with equality contstraints on rows.", "topics": [ "volnmf_simplex_row" ] } ], "_readme": "https://github.com/kharchenkolab/vrnmf/raw/HEAD/README.md", "_rundeps": [ "ica", "lattice", "lpSolveAPI", "Matrix", "nnls", "quadprog" ], "_score": 4.369215857410143, "_indexed": true, "_nocasepkg": "vrnmf", "_universes": [ "kharchenkolab", "evanbiederstedt" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.2", "date": "2026-10-19T08:08:00.000Z", "distro": "resolute", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/631666a52021a68e6b4748346a226be7900e2751644beac2d4404a8993f12904", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.6.1", "os": "linux", "version": "1.0.2", "date": "2026-10-19T08:09:38.000Z", "distro": "resolute", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/7c80b6c2d1eeb88102f7bd145a16d1fb00494bff3b255ccbbf7a69d34f5a9bf7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.5.3", "os": "mac", "version": "1.0.2", "date": "2026-10-19T08:09:03.000Z", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/c5c2a00a6b4e7cb69f36d3af731ea29f07ef3687d58c6a9d333d8e6af54736f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.6.1", "os": "mac", "version": "1.0.2", "date": "2026-10-19T08:08:30.000Z", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/e4c757139110c9f4edb8315f5fb75945a532b2805142294eff4115e1a93b3066", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.2", "date": "2026-10-19T08:10:27.000Z", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/415617b12f3f3b1f91811a02cec2223fdeccd0a220692defd9557e009b38092a", "status": "success", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.7.0", "os": "win", "version": "1.0.2", "date": "2026-10-19T08:07:27.000Z", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/04252b92d47f16f790fd267d075e3906e545b077f768efa2b0fd3fa18a86f0b2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.5.3", "os": "win", "version": "1.0.2", "date": "2026-10-19T08:07:29.000Z", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/bc4737a75bbba8b2c4b6654b9cbb245fcc8a9874205817ec16ae74daf52a9bd9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" }, { "r": "4.6.1", "os": "win", "version": "1.0.2", "date": "2026-10-19T08:11:20.000Z", "commit": "968a29eddad04b92cee7b8067b504082b31d53f8", "fileid": "https://r2.ropensci.org/d37b1e56f27e69d8c698a89430c623458f009473d0262f6f949b4e2da3a1bd8d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kharchenkolab/actions/runs/39219682715" } ] }