{ "_id": "6abbb2ef99f7aa8c6aa484ed", "Package": "coglasso", "Type": "Package", "Title": "Collaborative Graphical Lasso - Multi-Omics Network\nReconstruction", "Version": "1.1.1.9000", "Authors@R": "c(\nperson(\"Alessio\", \"Albanese\", email = \"alessio.albanese@wur.nl\", role = c(\"aut\", \"cre\", \"cph\"), comment=c(ORCID = \"0000-0003-1783-5613\")),\nperson(\"Pariya\", \"Behrouzi\", email = \"pariya.behrouzi@wur.nl\", role = c(\"aut\"), comment=c(ORCID = \"0000-0001-6762-5433\")))", "Description": "Reconstruct networks from multi-omics data sets with the\ncollaborative graphical lasso (coglasso) algorithm described in\nAlbanese, A., Kohlen, W., and Behrouzi, P. (2026)\n. Use the main wrapper\nfunction `bs()` to build and select a multi-omics network.", "URL": "https://github.com/DrQuestion/coglasso,\nhttps://drquestion.github.io/coglasso/", "BugReports": "https://github.com/DrQuestion/coglasso/issues", "License": "GPL (>= 2)", "LazyData": "true", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://drquestion.r-universe.dev", "Date/Publication": "2026-07-31 13:24:22 UTC", "RemoteUrl": "https://github.com/drquestion/coglasso", "RemoteRef": "HEAD", "RemoteSha": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-09-29 11:52:05 UTC", "User": "root" }, "Author": "Alessio Albanese [aut, cre, cph] (ORCID:\n),\nPariya Behrouzi [aut] (ORCID: )", "Maintainer": "Alessio Albanese ", "_user": "drquestion", "_type": "src", "_file": "coglasso_1.1.1.9000.tar.gz", "_fileid": "https://r2.ropensci.org/4359fe4c168152d40f0d9e19d1b461395032b8bd66d535482af1ffea5795af9b", "_filesize": 402652, "_sha256": "4359fe4c168152d40f0d9e19d1b461395032b8bd66d535482af1ffea5795af9b", "_expires": "2027-01-07T12:45:33.000Z", "_created": "2026-09-29T11:52:05.000Z", "_published": "2026-09-29T12:45:35.369Z", "_jobs": [ { "job": 109392933529, "time": 159, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11031666640" }, { "job": 109392933540, "time": 200, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11031865153" }, { "job": 109392933662, "time": 154, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11031032994" }, { "job": 109392933563, "time": 186, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11031805262" }, { "job": 109392933478, "time": 231, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11033641467" }, { "job": 109392933588, "time": 295, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11033257455" }, { "job": 109392933571, "time": 233, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11033162251" }, { "job": 109392933471, "time": 442, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11033682171" }, { "job": 109391350723, "time": 273, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11031501443" }, { "job": 109392933399, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11031221982" }, { "job": 109392933504, "time": 364, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11030993328" }, { "job": 109392933533, "time": 201, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11031217182" }, { "job": 109392933507, "time": 168, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11031551867" }, { "job": 109392933495, "time": 366, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11030899914" }, { "job": 109392933573, "time": 155, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11031018069" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824", "_status": "success", "_upstream": "https://github.com/drquestion/coglasso", "_commit": { "id": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "author": "DrQuestion ", "committer": "DrQuestion ", "message": "Increment version number to 1.1.1.9000\n", "time": 1785504262 }, "_maintainer": { "name": "Alessio Albanese", "email": "alessio.albanese@wur.nl", "login": "drquestion", "bluesky": "@doctorquestion.bsky.social", "linkedin": "in/alessioalbanese", "twitter": "@drquestion97", "description": "On my way to discover how plant roots nodulate 🌱 powered by graphical modelling πŸ•ΈοΈπŸ’₯ ", "uuid": 32851526, "orcid": "0000-0003-1783-5613" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "igraph", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.11", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "drquestion", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 5 }, { "week": "2026-31", "n": 6 } ], "_tags": [ { "name": "v1.1.0", "date": "2025-10-28" }, { "name": "v1.1.1", "date": "2026-07-29" } ], "_stars": 5, "_contributors": [ { "user": "drquestion", "count": 75, "uuid": 32851526 } ], "_userbio": { "uuid": 32851526, "type": "user", "name": "Alessio Albanese", "followers": 9, "description": "On my way to discover how plant roots nodulate 🌱 powered by graphical modelling πŸ•ΈοΈπŸ’₯ " }, "_downloads": { "count": 399, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/coglasso" }, "_devurl": "https://github.com/drquestion/coglasso", "_pkgdown": "https://drquestion.github.io/coglasso/", "_searchresults": 0, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/coglasso.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/drquestion/coglasso", "_realowner": "drquestion", "_cranurl": true, "_releases": [ { "version": "1.0.2", "date": "2024-04-03" }, { "version": "1.1.0", "date": "2025-10-28" }, { "version": "1.1.1", "date": "2026-07-30" } ], "_exports": [ "bs", "coglasso", "get_network", "get_pcor", "select_coglasso", "stars_coglasso", "xestars", "xstars" ], "_datasets": [ { "name": "multi_omics_sd", "title": "Multi-omics dataset of sleep deprivation in mouse", "object": "multi_omics_sd", "class": [ "matrix", "array" ], "fields": [ "Plin4", "Arc", "Egr2", "Tekt4", "Fos", "Plekhg4", "Slco1b2", "Gh", "Tnfrsf25", "Misp", "Rtp1", "1700102P08Rik", "Fosb", "Maff", "Tm6sf2", "Sdf2l1", "Bace2", "Cdkn1a", "Klhdc9", "Noxred1", "Rasd1", "Lrrc29", "Fam83d", "Egr3", "Timp1", "Nr4a1", "Serinc2", "Dusp4", "Tmem252", "Sik1", "Npas4", "Samd3", "Trib1", "Cbln4", "0610040B10Rik", "1700001L05Rik", "Hspb1", "Fosl2", "Mybpc3", "Rasl11a", "Dok3", "Gkn3", "Parpbp", "Dio2", "Egr1", "Cml5", "Gpr3", "Acr", "Gm1141", "B430319G15Rik", "Zglp1", "Slc23a3", "Stac3", "Cstad", "Hspa1b", "Htr5b", "Hspa5", "Fam150b", "Cyr61", "Map3k6", "Dusp5", "Gck", "Itga10", "Alox12", "Cirbp", "Ptgs2", "Mdga1", "Cd28", "Neurog2", "Hist1h2be", "Fat2", "Pglyrp1", "Gm16062", "Hif3a", "Arl4d", "8430408G22Rik", "Hist2h3c1", "Derl3", "BC021891", "A730020M07Rik", "Junb", "Arhgef33", "Pcsk9", "Mir6982", "Npbwr1", "Pla2g4e", "Nr4a3", "Insl5", "Vwa3a", "AW549542", "Map3k19", "Spry4", "Espnl", "Tmem82", "Gli1", "Tmod4", "Hfe2", "4930426L09Rik", "Nlrc4", "Rho", "P4ha1", "Cryab", "Fam46a", "Chordc1", "Dusp6", "Sfpq", "Mkks", "Rbm3", "Trim9", "Etv5", "Cys1", "Tra2a", "Dusp1", "Spred1", "Usp2", "Creld2", "Nfil3", "Xbp1", "Calr", "Dusp11", "Hspa1a", "Pdia6", "Opalin", "Hsp90b1", "Hexim1", "Hsph1", "Pllp", "Eny2", "Homer1", "Manf", "Dnajb1", "Lrrk2", "Slc5a3", "Arl4a", "Synj2", "Bcl2", "Pdia3", "Enc1", "Zbtb40", "Zbtb22", "Mfsd4", "Pdp1", "Tipin", "Ier5", "Dnaja4", "Dnajb11", "Pcsk1", "Gfod1", "Sik2", "Dnajc3", "Pfkfb3", "Hspa4l", "Tubd1", "BC004004", "Stip1", "Fkbp4", "Rbm11", "Otub2", "Mettl16", "Luzp1", "Trib2", "Tfrc", "Ala", "Arg", "Asn", "Cit", "Gln", "Glu", "Gly", "His", "Ile", "Leu", "Lys", "Met", "Orn", "Phe", "Pro", "Ser", "Thr", "Trp", "Tyr", "Val", "Putrescine", "Spermidine", "t4-OH-Pro", "SDMA", "C0", "C14:1", "C18:1", "C18:2", "C2", "lysoPC a C17:0", "lysoPC a C18:2", "lysoPC a C20:3", "PC aa C32:0", "PC aa C34:2", "PC aa C34:4", "PC aa C36:0", "PC aa C36:2", "PC aa C36:3", "PC aa C36:5", "PC aa C36:6", "PC aa C38:4", "PC aa C40:2", "PC aa C40:3", "PC aa C40:4", "PC aa C42:2", "PC aa C42:4", "PC aa C42:6", "PC ae C32:1", "PC ae C32:2", "PC ae C34:0", "PC ae C34:2", "PC ae C36:2", "PC ae C36:3", "PC ae C36:5", "PC ae C38:2", "PC ae C38:3", "PC ae C40:1", "PC ae C40:2", "PC ae C42:0", "PC ae C42:1", "PC ae C42:2", "PC ae C42:3", "PC ae C42:4", "PC ae C44:4", "PC ae C44:5", "SM (OH) C14:1", "SM (OH) C16:1", "SM (OH) C22:1", "SM (OH) C22:2", "SM (OH) C24:1", "SM C16:0", "SM C16:1", "SM C18:0", "SM C18:1", "SM C24:0", "SM C24:1" ], "rows": 30, "table": true, "tojson": true }, { "name": "multi_omics_sd_micro", "title": "Multi-omics dataset of sleep deprivation in mouse", "object": "multi_omics_sd_micro", "class": [ "matrix", "array" ], "fields": [ "Cirbp", "Hspa5", "Hsp90b1", "Dnajb11", "Trp", "PC aa C36:3" ], "rows": 30, "table": true, "tojson": true }, { "name": "multi_omics_sd_small", "title": "Multi-omics dataset of sleep deprivation in mouse", "object": "multi_omics_sd_small", "class": [ "matrix", "array" ], "fields": [ "Cirbp", "Hspa5", "P4ha1", "Spred1", "Creld2", "Pdia6", "Hsp90b1", "Hsph1", "Manf", "Pdia3", "Dnajb11", "Dnajc3", "BC004004", "Stip1", "Phe", "Trp", "Putrescine", "PC aa C36:3", "PC ae C32:2" ], "rows": 30, "table": true, "tojson": true } ], "_help": [ { "page": "bs", "title": "Build multiple networks and select the best one from a multi-omics data set", "topics": [ "bs" ] }, { "page": "coglasso", "title": "Estimate networks from a multi-omics data set", "topics": [ "coglasso" ] }, { "page": "get_network", "title": "Extract a 'coglasso' network", "topics": [ "get_network" ] }, { "page": "get_pcor", "title": "Extract a 'coglasso' partial correlation matrix", "topics": [ "get_pcor" ] }, { "page": "multi_omics_sd", "title": "Multi-omics dataset of sleep deprivation in mouse", "topics": [ "multi_omics_sd", "multi_omics_sd_micro", "multi_omics_sd_small" ] }, { "page": "plot.select_coglasso", "title": "Plot selected 'coglasso' networks", "topics": [ "plot.coglasso", "plot.select_coglasso" ] }, { "page": "select_coglasso", "title": "Select the best 'coglasso' network", "topics": [ "select_coglasso" ] }, { "page": "xestars", "title": "Efficient stability selection of the best 'coglasso' network", "topics": [ "xestars" ] }, { "page": "xstars", "title": "Stability selection of the best 'coglasso' network", "topics": [ "xstars" ] } ], "_pkglogo": "https://github.com/drquestion/coglasso/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/drquestion/coglasso/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "Rcpp", "RcppEigen", "rlang", "vctrs", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "coglasso.Rmd", "filename": "coglasso.html", "title": "Reconstructing mult-omics networks with coglasso", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Multi-omics network reconstruction", "References" ], "created": "2023-11-07 11:36:03", "modified": "2026-07-27 12:43:11", "commits": 14 }, { "source": "manuscript.Rmd", "filename": "manuscript.html", "title": "Reproduction of manuscript's results", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Reproducing the results", "References" ], "created": "2023-11-08 15:21:46", "modified": "2026-07-27 12:43:11", "commits": 9 } ], "_score": 5.176091259055681, "_indexed": true, "_nocasepkg": "coglasso", "_universes": [ "drquestion" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.1.9000", "date": "2026-09-29T11:54:28.000Z", "distro": "resolute", "arch": "aarch64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/c3e01dc1dee620c2be437731d75f733da0b4520c4535b2e663e7982104c13e48", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.7.0", "os": "linux", "version": "1.1.1.9000", "date": "2026-09-29T11:54:41.000Z", "distro": "resolute", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/52b394a910971ac36fe9a323f24e35684f144bc948a1efc5975ffad8ff4e486e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1.9000", "date": "2026-09-29T11:54:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/b5b3b436d6671c6fdeb0497ebed5e2147be8e30b13dc54efbc2700b9eae630a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.1", "os": "linux", "version": "1.1.1.9000", "date": "2026-09-29T11:54:35.000Z", "distro": "resolute", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/158ad81de62d9e3cd44186eda6d28bb992be6bde9ecc29e27c42e8fc4665c6f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1.9000", "date": "2026-09-29T12:39:59.000Z", "arch": "aarch64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/f0952fcb7193300d43171ce9f3c6de1537a476a153eed44f0cb60fb80af9b4fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.5.3", "os": "mac", "version": "1.1.1.9000", "date": "2026-09-29T12:42:38.000Z", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/921c4e68a7850124f78903bc2c31578dd2d2a4f939d8156f23fa629dc5486a17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.1", "os": "mac", "version": "1.1.1.9000", "date": "2026-09-29T12:40:31.000Z", "arch": "aarch64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/ffd2e330437afa594771a93803dd806f7a5626c869388dde13353df1fcee6355", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.1", "os": "mac", "version": "1.1.1.9000", "date": "2026-09-29T12:42:23.000Z", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/d5e68d0942518d194d4f971265c9a849fbb7a7e68b3c79a0583c55d5edb9ad9f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.1.9000", "date": "2026-09-29T11:54:42.000Z", "arch": "emscripten", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/c6a04513592415e0a809d402f4161e7fa30a84f9c28717b9beb354945adb7167", "status": "success", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.7.0", "os": "win", "version": "1.1.1.9000", "date": "2026-09-29T11:57:17.000Z", "arch": "aarch64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/06344ec8a98604a6f233d34eec1a930a4b4538b14c19d2f192382be068df7c35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.7.0", "os": "win", "version": "1.1.1.9000", "date": "2026-09-29T11:53:34.000Z", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/1cb61ac0fbf693f9e27f9939d0c244c7a73e83afdd005e5a4ffc6fe252671abd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.5.3", "os": "win", "version": "1.1.1.9000", "date": "2026-09-29T11:53:38.000Z", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/9e3bfa114c992b529823586259fdde2df375f33a5a029508dd2fdbee97e0bceb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.1", "os": "win", "version": "1.1.1.9000", "date": "2026-09-29T11:57:07.000Z", "arch": "aarch64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/5ec746fa548dd14349acbf14259b0ba4157310f46175acf22a55c4bdfbdb50a3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" }, { "r": "4.6.1", "os": "win", "version": "1.1.1.9000", "date": "2026-09-29T11:53:33.000Z", "arch": "x86_64", "commit": "59dfb8808026fa64b848eb3855c362c3cd0fdc5b", "fileid": "https://r2.ropensci.org/0851c8a9456adafece2bc200eca038ce5f1dfb18cf2ee8e769e2ed510c4df002", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/drquestion/actions/runs/36563950824" } ] }