{ "_id": "6acce83aa14063b82c3aa5ed", "Package": "GeneNMF", "Type": "Package", "Title": "Non-Negative Matrix Factorization for Single-Cell Omics", "Version": "0.9.99", "Authors@R": "c(\nperson('Massimo', 'Andreatta',\nemail = 'massimo.andreatta@unige.ch',\nrole = c('aut','cre'),\ncomment = c(ORCID = '0000-0002-8036-2647')),\nperson('Santiago', 'Carmona',\nemail = 'santiago.carmona@unige.ch',\nrole = c('aut'),\ncomment = c(ORCID = '0000-0002-2495-0671'))\n)", "Description": "A collection of methods to extract gene programs from\nsingle-cell gene expression data using non-negative matrix\nfactorization (NMF). 'GeneNMF' contains functions to directly\ninteract with the 'Seurat' toolkit and derive interpretable\ngene program signatures.", "biocViews": "", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://github.com/carmonalab/GeneNMF", "BugReports": "https://github.com/carmonalab/GeneNMF/issues", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://carmonalab.r-universe.dev", "Date/Publication": "2026-10-12 13:46:18 UTC", "RemoteUrl": "https://github.com/carmonalab/GeneNMF", "RemoteRef": "HEAD", "RemoteSha": "587bc82e735d60124507ce68342889dbf163f366", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-12 13:55:13 UTC", "User": "root" }, "Author": "Massimo Andreatta [aut, cre] (ORCID:\n),\nSantiago Carmona [aut] (ORCID: )", "Maintainer": "Massimo Andreatta ", "_user": "carmonalab", "_type": "src", "_file": "GeneNMF_0.9.99.tar.gz", "_fileid": "https://r2.ropensci.org/547fe741ee7fb5f009ce4f8cad06e6c01749741f57b4501e0feabec045c3ccae", "_filesize": 706068, "_sha256": "547fe741ee7fb5f009ce4f8cad06e6c01749741f57b4501e0feabec045c3ccae", "_expires": "2027-01-20T14:01:28.000Z", "_created": "2026-10-12T13:55:13.000Z", "_published": "2026-10-12T14:01:30.152Z", "_buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 114844976976, "time": 313, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11752406039" }, { "job": 114844976813, "time": 315, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11751098984" }, { "job": 114844977005, "time": 194, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11751278248" }, { "job": 114844976842, "time": 205, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11751033682" }, { "job": 114843078168, "time": 273, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11751996092" }, { "job": 114844976818, "time": 157, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11750988743" }, { "job": 114844976843, "time": 229, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11751946856" }, { "job": 114844977083, "time": 226, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11751522687" }, { "job": 114844976872, "time": 201, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11752231497" } ], "_upstream": "https://github.com/carmonalab/GeneNMF", "_commit": { "id": "587bc82e735d60124507ce68342889dbf163f366", "author": "mass-a ", "committer": "mass-a ", "message": "Add tests; + bug fixes\n", "time": 1791812778 }, "_maintainer": { "name": "Massimo Andreatta", "email": "massimo.andreatta@unige.ch", "login": "mass-a", "orcid": "0000-0002-8036-2647", "description": "", "uuid": 56030596 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "RcppML", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.3.0", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "lsa", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "dendextend", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "colorspace", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "fgsea", "role": "Suggests" }, { "package": "msigdbr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "carmonalab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 1 }, { "week": "2026-21", "n": 3 }, { "week": "2026-23", "n": 1 }, { "week": "2026-30", "n": 4 }, { "week": "2026-42", "n": 1 } ], "_tags": [], "_stars": 211, "_contributors": [ { "user": "mass-a", "count": 110, "uuid": 56030596 }, { "user": "sjcarmona", "count": 22, "uuid": 7525176 }, { "user": "maozhy3", "count": 2, "uuid": 46839266 }, { "user": "liuzhenyu-yyy", "count": 1, "uuid": 37285516 } ], "_userbio": { "uuid": 48469311, "type": "organization", "name": "Cancer Systems Immunology Lab", "followers": 149, "description": "Single-cell omics data science at the Department of Pathology of Immunology of the University of Geneva" }, "_downloads": { "count": 691, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GeneNMF" }, "_devurl": "https://github.com/carmonalab/genenmf", "_searchresults": 64, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeneNMF.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/carmonalab/genenmf", "_realowner": "carmonalab", "_cranurl": true, "_releases": [ { "version": "0.4.0", "date": "2024-02-29" }, { "version": "0.6.0", "date": "2024-07-22" }, { "version": "0.6.2", "date": "2024-11-14" }, { "version": "0.8.0", "date": "2025-04-24" }, { "version": "0.9.2", "date": "2025-09-11" } ], "_exports": [ "dropMetaPrograms", "findVariableFeatures_wfilters", "getDataMatrix", "getMetaPrograms", "getNMFgenes", "multiNMF", "plotMetaPrograms", "renameMetaPrograms", "runGSEA", "runNMF" ], "_datasets": [ { "name": "sampleObj", "title": "Sample dataset to test GeneNMF installation", "object": "sampleObj", "class": [ "Seurat" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dropMetaPrograms", "title": "Drop meta-programs", "topics": [ "dropMetaPrograms" ] }, { "page": "findVariableFeatures_wfilters", "title": "Find variable features", "topics": [ "findVariableFeatures_wfilters" ] }, { "page": "getDataMatrix", "title": "Extract data matrix from Seurat object", "topics": [ "getDataMatrix" ] }, { "page": "getMetaPrograms", "title": "Extract consensus gene programs (meta-programs)", "topics": [ "getMetaPrograms" ] }, { "page": "getNMFgenes", "title": "Get list of genes for each NMF program", "topics": [ "getNMFgenes" ] }, { "page": "multiNMF", "title": "Run NMF on a list of Seurat objects", "topics": [ "multiNMF" ] }, { "page": "plotMetaPrograms", "title": "Visualizations for meta-programs", "topics": [ "plotMetaPrograms" ] }, { "page": "renameMetaPrograms", "title": "Rename meta-programs", "topics": [ "renameMetaPrograms" ] }, { "page": "runGSEA", "title": "Run gene-set overrepresentation analysis", "topics": [ "runGSEA" ] }, { "page": "runNMF", "title": "Compute NMF as a low-dim embedding for Seurat", "topics": [ "runNMF" ] }, { "page": "sampleObj", "title": "Sample dataset to test GeneNMF installation", "topics": [ "sampleObj" ] } ], "_readme": "https://github.com/carmonalab/GeneNMF/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "bitops", "bslib", "cachem", "caTools", "cli", "cluster", "codetools", "colorspace", "commonmark", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "deldir", "dendextend", "digest", "dotCall64", "dplyr", "dqrng", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "fs", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lmtest", "lsa", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pheatmap", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "progressr", "promises", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppML", "RcppProgress", "RcppThread", "RcppTOML", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "Rtsne", "S7", "sass", "scales", "scattermore", "sctransform", "Seurat", "SeuratObject", "shiny", "sitmo", "SnowballC", "sourcetools", "sp", "spam", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "survival", "sys", "tensor", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "uwot", "vctrs", "viridis", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "make.index.Rmd", "filename": "make.index.html", "title": "Index of GeneNMF vignettes", "author": "M. Andreatta, S. Carmona", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-02-27 14:25:56", "modified": "2024-07-19 11:10:27", "commits": 3 } ], "_score": 8.00552369267328, "_indexed": true, "_nocasepkg": "genenmf", "_universes": [ "carmonalab", "mass-a" ], "_previous": "0.9.6", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.9.99", "date": "2026-10-12T13:58:51.000Z", "distro": "resolute", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/4f613409fff2692ab55f83ebfc21e6850b27c9acec3d04f93762b37416532ef2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.6.1", "os": "linux", "version": "0.9.99", "date": "2026-10-12T13:58:58.000Z", "distro": "resolute", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/a951d3d4f13f062363341d132072bb3375a12f0b820930d46131508527fefa35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.5.3", "os": "mac", "version": "0.9.99", "date": "2026-10-12T13:57:24.000Z", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/f09c26d998b65356eff40bf1c6bccbfa8c695487e2551925bfe03a90f2713a75", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.6.1", "os": "mac", "version": "0.9.99", "date": "2026-10-12T13:57:35.000Z", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/fa221b693469924991ff7e1c6d1bc9b1e32968174149b1880c7a122f4c2a005a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.6.0", "os": "wasm", "version": "0.9.99", "date": "2026-10-12T13:58:15.000Z", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/40e452006f2ae3540618668b4ad1b8f061b336edd4fc1abce8251593f96000ea", "status": "success", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.7.0", "os": "win", "version": "0.9.99", "date": "2026-10-12T13:57:05.000Z", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/8410504ad627bc4e1a2b210246364721e611f7bab2dc7e7187d2eb097a2a00b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.5.3", "os": "win", "version": "0.9.99", "date": "2026-10-12T13:57:12.000Z", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/e26b4e84e8dd067c9259dfce2590b971617f174f65ba69d5f1e3604c4d7a734d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" }, { "r": "4.6.1", "os": "win", "version": "0.9.99", "date": "2026-10-12T13:56:49.000Z", "commit": "587bc82e735d60124507ce68342889dbf163f366", "fileid": "https://r2.ropensci.org/c6485326aa3c9cfeee388318e3d5bcdee0b7c68dcddfd84fc931c27451ca6745", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/carmonalab/actions/runs/38258580802" } ] }