{ "_id": "6a1955f0acfb0bcc41de19d0", "Package": "iModMix", "Title": "Integrative Modules for Multi-Omics Data", "Version": "1.2.0", "Authors@R": "c(\nperson(given = \"Isis\",\nfamily = \"Narvaez-Bandera\",\nrole = c(\"aut\", \"cre\"),\nemail = \"isis.narvaez@upr.edu\",\ncomment = c(ORCID = \"0000-0001-7320-618X\")))", "Description": "The iModMix network-based method offers an integrated\nframework for analyzing multi-omics data, including\nmetabolomics, proteomics, and transcriptomics data, enabling\nthe exploration of intricate molecular associations within\nheterogeneous biological systems.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "biocViews": "Software, Network, Clustering, Visualization,\nTranscriptomics, Proteomics, Metabolomics, GeneExpression,\nPrincipalComponent", "URL": "https://github.com/biodatalab/iModMix", "BugReports": "https://github.com/biodatalab/iModMix/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev perl zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:05:47 UTC", "RemoteUrl": "https://github.com/bioc/iModMix", "RemoteRef": "RELEASE_3_23", "RemoteSha": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:48:51 UTC", "User": "root" }, "Author": "Isis Narvaez-Bandera [aut, cre] (ORCID:\n)", "Maintainer": "Isis Narvaez-Bandera ", "MD5sum": "b2d1a8ae4cb3b3c9704502661fc8ae30", "_user": "bioc-release", "_type": "src", "_file": "iModMix_1.2.0.tar.gz", "_fileid": "c8b27017d28e95629449c730c2d4a437c42bb0a3ac566eae7e30b5b9e52a7392", "_filesize": 10672934, "_sha256": "c8b27017d28e95629449c730c2d4a437c42bb0a3ac566eae7e30b5b9e52a7392", "_created": "2026-05-29T07:48:51.000Z", "_published": "2026-05-29T09:01:36.134Z", "_jobs": [ { "job": 78460040828, "time": 206, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285811076" }, { "job": 78460040843, "time": 238, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285820355" }, { "job": 78460040876, "time": 228, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285817547" }, { "job": 78460040866, "time": 126, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7286862411" }, { "job": 78460040859, "time": 93, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7287008285" }, { "job": 78459402382, "time": 273, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285751558" }, { "job": 78460040842, "time": 179, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285803566" }, { "job": 78460040919, "time": 126, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285789167" }, { "job": 78460040853, "time": 115, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285785600" }, { "job": 78460040863, "time": 125, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285788315" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/iModMix", "_commit": { "id": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381547 }, "_maintainer": { "name": "Isis Narvaez-Bandera", "email": "isis.narvaez@upr.edu", "login": "isisnarvaez", "description": "", "uuid": 34428713, "orcid": "0000-0001-7320-618X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "config", "version": ">= 0.3.2", "role": "Imports" }, { "package": "golem", "version": ">= 0.4.1", "role": "Imports" }, { "package": "shiny", "version": ">= 1.7.5", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "WGCNA", "role": "Imports" }, { "package": "corrplot", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "dynamicTreeCut", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glassoFast", "role": "Imports" }, { "package": "impute", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "visNetwork", "role": "Imports" }, { "package": "shinyBS", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "iModMixData", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "ExperimentHub", "version": ">= 2.99.0", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "ggfortify", "role": "Suggests" }, { "package": "shinyWidgets", "role": "Suggests" }, { "package": "pROC", "role": "Suggests" }, { "package": "tuneR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "curl", "role": "Suggests" }, { "package": "readxl", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "vroom", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "enrichR", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-34", "n": 2 }, { "week": "2025-35", "n": 1 }, { "week": "2025-36", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-38", "n": 3 }, { "week": "2025-41", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-10", "n": 3 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "software", "network", "clustering", "visualization", "transcriptomics", "proteomics", "metabolomics", "geneexpression", "principalcomponent", "bioinformatics", "multiomics" ], "_stars": 4, "_contributors": [ { "user": "isisnarvaez", "count": 148, "uuid": 34428713 }, { "user": "ashleylui", "count": 17, "uuid": 79220759 }, { "user": "gonzalg-moffitt", "count": 1, "uuid": 87827748 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 231, "source": "https://www.bioconductor.org/packages/stats/bioc/iModMix" }, "_devurl": "https://github.com/biodatalab/imodmix", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/iModMix.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/biodatalab/imodmix", "_realowner": "bioc", "_cranurl": false, "_exports": [ "fctAssignmentGenesEnrichr", "fctClusterAssignments", "fctEigengenes", "fctFeaturesAnnotCorrelation", "fctHierarchicalCluster", "fctiModMix2SE", "fctLoadData", "fctModulesCorrelation", "fctPartialCors", "fctPerformClassification", "run_app" ], "_help": [ { "page": "fctAssignmentGenesEnrichr", "title": "fctAssignmentGenesEnrichr", "topics": [ "fctAssignmentGenesEnrichr" ] }, { "page": "fctClusterAssignments", "title": "fctClusterAssignments", "topics": [ "fctClusterAssignments" ] }, { "page": "fctEigengenes", "title": "fctEigengenes", "topics": [ "fctEigengenes" ] }, { "page": "fctFeaturesAnnotCorrelation", "title": "fctFeaturesAnnotCorrelation", "topics": [ "fctFeaturesAnnotCorrelation" ] }, { "page": "fctHierarchicalCluster", "title": "fctHierarchicalCluster", "topics": [ "fctHierarchicalCluster" ] }, { "page": "fctiModMix2SE", "title": "fctiModMix2SE", "topics": [ "fctiModMix2SE" ] }, { "page": "fctLoadData", "title": "fctLoadData", "topics": [ "fctLoadData" ] }, { "page": "fctModulesCorrelation", "title": "fctModulesCorrelation", "topics": [ "fctModulesCorrelation" ] }, { "page": "fctPartialCors", "title": "fctPartialCors", "topics": [ "fctPartialCors" ] }, { "page": "fctPerformClassification", "title": "fctPerformClassification", "topics": [ "fctPerformClassification" ] }, { "page": "run_app", "title": "Run the Shiny Application", "topics": [ "run_app" ] } ], "_readme": "https://github.com/bioc/iModMix/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "askpass", "attempt", "backports", "base64enc", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "checkmate", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "commonmark", "ComplexHeatmap", "config", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "doParallel", "dplyr", "DT", "dynamicTreeCut", "evaluate", "ExperimentHub", "farver", "fastcluster", "fastmap", "filelock", "fontawesome", "foreach", "foreign", "Formula", "fs", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "glassoFast", "GlobalOptions", "glue", "golem", "gridExtra", "gtable", "here", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "iModMixData", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "otel", "pillar", "pkgconfig", "png", "preprocessCore", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rjson", "rlang", "rmarkdown", "rpart", "rprojroot", "RSQLite", "rstudioapi", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shape", "shiny", "shinyBS", "sourcetools", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "visNetwork", "WGCNA", "withr", "xfun", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "iModMixTutorial.Rmd", "filename": "iModMixTutorial.html", "title": "iModMix -integrative Modules for Multi-omics data", "author": "Isis Narvaez-Bandera", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Download the package from Bioconductor", "Load the package into R session", "Launching the iModMix Shiny App", "Launch the app locally", "Access the app online", "Example to integrate 2 omics datasets", "Generate modules", "Load expression Data 1 and metadata from clear cell renal cell carcinoma", "Perform preprocessing of data", "Perform Partial correlation analysis, network construction and module eigengene calculation", "Load expression Data 2 and perform partial correlation analysis, network construction and module eigengene calculation", "Relate modules to phenotype", "Multi-omics analysis: Integration of Data 1 and Data 2", "Enrichment analysis using gene Symbol", "Working with Bioconductor's SummarizedExperiment class", "Session Information" ], "created": "2025-05-12 01:10:10", "modified": "2025-10-10 19:52:43", "commits": 12 } ], "_score": 5.6020599913279625, "_indexed": false, "_nocasepkg": "imodmix", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/iModMix", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0", "date": "2026-05-29T07:52:29.000Z", "distro": "noble", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "dbc6ded39aee6574089287584e2337c889978246d7f5bb372ce36f8dccc3cebb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.6.0", "os": "linux", "version": "1.2.0", "date": "2026-05-29T07:52:25.000Z", "distro": "noble", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "3835ea776f8ca7dadf019d32da9d708eab50d1b8371b0ea7921eb613dfa106d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0", "date": "2026-05-29T08:52:34.000Z", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "e7e0d90bdc651af2c77f44d75928ecbb90af5fd46525b1b508d6b2fb9c0bca01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.6.0", "os": "mac", "version": "1.2.0", "date": "2026-05-29T09:00:40.000Z", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "35c064b1e590cb47c4a9cc44866d347b40b8f58f9dd2880a7528e092b589988f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.0", "date": "2026-05-29T07:52:07.000Z", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "d618493d59b0b12f01c496bba9270fd780e1dd2addf02e4e0e662447622da0d7", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.7.0", "os": "win", "version": "1.2.0", "date": "2026-05-29T07:50:38.000Z", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "fe2d69bbd11c161b4ca773a15b8368b242a7992a9d57b72d902d833f27223077", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.5.3", "os": "win", "version": "1.2.0", "date": "2026-05-29T07:50:25.000Z", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "3cc379b2ccf54b7c01b9bd2e1f9f278a170ca7c2b07b7db66ae959fc86992741", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" }, { "r": "4.6.0", "os": "win", "version": "1.2.0", "date": "2026-05-29T07:50:35.000Z", "commit": "45dbc5c29a0aed0b50c7a1db378738f987e8281b", "fileid": "a9b0bbca8b63136b24f7f7f812b025a4077ca47801a5c9d68ad6017d24131ecf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624955524" } ] }