{ "_id": "6a1068d3acfb0bcc41ca9781", "Package": "M3JF", "Type": "Package", "Title": "Multi-Modal Matrix Joint Factorization for Integrative\nMulti-Omics Data Analysis", "Version": "0.1.0", "Date": "2023-07-25", "Authors@R": "person(\"Xiaoyao\", \"Yin\", role = c(\"aut\", \"cre\"), email = \"xyyin@xmail.ncba.ac.cn\")", "Description": "Multi modality data matrices are factorized conjointly\ninto the multiplication of a shared sub-matrix and multiple\nmodality specific sub-matrices, group sparse constraint is\napplied to the shared sub-matrix to capture the homogeneous and\nheterogeneous information, respectively. Then the samples are\nclassified by clustering the shared sub-matrix with kmeanspp(),\na new version of kmeans() developed here to obtain concordant\nresults. The package also provides the cluster number\nestimation by rotation cost. Moreover, cluster specific\nfeatures could be retrieved using hypergeometric tests.", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-08 04:54:58 UTC", "User": "root" }, "Author": "Xiaoyao Yin [aut, cre]", "Maintainer": "Xiaoyao Yin ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2023-08-14 08:30:39 UTC", "RemoteUrl": "https://github.com/cran/M3JF", "RemoteRef": "HEAD", "RemoteSha": "796c977d159a8c3e13df30188874c54717e8beee", "MD5sum": "56cbec33f3f34f6a82bbafa13f1b47e7", "_user": "cran", "_type": "src", "_file": "M3JF_0.1.0.tar.gz", "_fileid": "47b71375ab146ba227af8e79f536c0578db005d6bf24bc89d2737db130ab7bf8", "_filesize": 128920, "_sha256": "47b71375ab146ba227af8e79f536c0578db005d6bf24bc89d2737db130ab7bf8", "_created": "2026-05-08T04:54:58.000Z", "_published": "2026-05-22T14:31:47.800Z", "_distro": "noble", "_jobs": [ { "job": 77400490521, "time": 156, "config": 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"dplyr", "role": "Imports" }, { "package": "InterSIM", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 183, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/M3JF" }, "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/M3JF.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2023-08-14" } ], "_exports": [ "cost", "crimmix_data_gen", "feature_screen_sd", "feature_selection", "initialize_WL", "iNMF_data_gen", "intersim_data_gen", "kmeanspp", "M3JF", "RotationCostBestGivenGraph", "simulateY", "update_E", "update_H" ], "_help": [ { "page": "cost", "title": "Calculate the cost defined by the objective function", "topics": [ "cost" ] }, { "page": "crimmix_data_gen", "title": "Generate the simulated dataset with three modalities with the package crimmix", "topics": [ "crimmix_data_gen" ] }, { "page": "feature_screen_sd", "title": "Screen the cluster related features via hypergeometric test p value and distribution standard derivation", "topics": [ "feature_screen_sd" ] }, { "page": "feature_selection", "title": "Select the cluster related features via hypergeometric test", "topics": [ "feature_selection" ] }, { "page": "initialize_WL", "title": "Initialize the shared sub-matrix E and modality specific sub-matrices list Hi", "topics": [ "initialize_WL" ] }, { "page": "iNMF_data_gen", "title": "Generate the simulated dataset with three modalities as the work iNMF", "topics": [ "iNMF_data_gen" ] }, { "page": "intersim_data_gen", "title": "Generate the simulated dataset with three modalities with the package InterSIM", "topics": [ "intersim_data_gen" ] }, { "page": "kmeanspp", "title": "A new version of kmeans that generates stable cluster result", "topics": [ "kmeanspp" ] }, { "page": "M3JF", "title": "Multi-Modal Matrix Joint Factorization", "topics": [ "M3JF" ] }, { "page": "RotationCostBestGivenGraph", "title": "Evaluate the cluster number of multiple modality data", "topics": [ "RotationCostBestGivenGraph" ] }, { "page": "simulateY", "title": "Generate the simulated dataset with specified parameters", "topics": [ "simulateY" ] }, { "page": "update_E", "title": "Update sub-matrix E", "topics": [ "update_E" ] }, { "page": "update_H", "title": "Update sub-matrices list Hi", "topics": [ "update_H" ] } ], "_rundeps": [ "alluvial", "Biobase", "BiocGenerics", "BiocManager", "cli", "cluster", "codetools", "colorspace", "cpp11", "digest", "doParallel", "dplyr", "ExPosition", "farver", 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