{ "_id": "6adface295167d9b9260cad3", "Package": "MacrophageFramework", "Type": "Package", "Title": "Multidimensional Macrophage Profiling", "Version": "0.99.0", "Authors@R": "person(\n\"Alessandro\", \"Palma\",\nemail = \"alessandro.palma2@uniroma1.it\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-1300-5479\")\n)", "Description": "Provides a multidimensional computational framework for\nmacrophage profiling based on an ontology of biological\nprograms. The framework independently detects macrophage\npopulations and characterizes their lineage-associated and\nfunctional-state programs using program-level expression\nscores, detection coverage, gene-program coherence, cluster\nprofiles, and profile similarity. The framework is designed to\ncapture continuous and combinatorial macrophage states without\nimposing binary activation categories.", "License": "GPL-3", "URL": "https://github.com/AlessandroPalma-hub/MacrophageFramework", "BugReports": "https://github.com/AlessandroPalma-hub/MacrophageFramework/issues", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "biocViews": "GeneExpression, ImmunoOncology, SingleCell, Software,\nVisualization", "RoxygenNote": "8.0.0", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-10-26 15:15:27 UTC", "RemoteUrl": "https://github.com/BiocStaging/MacrophageFramework", "RemoteRef": "HEAD", "RemoteSha": "34082803510846696ed9fb860eee3dd83ccdd629", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-26 19:35:17 UTC", "User": "root" }, "Author": "Alessandro Palma [aut, cre, cph] (ORCID:\n)", "Maintainer": "Alessandro Palma ", "_user": "biocstaging", "_type": "src", "_file": "MacrophageFramework_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/e1ec93b3d5b86413f9330dc214da80b83fa959660ea3186deea3990cac404136", "_filesize": 8692988, "_sha256": "e1ec93b3d5b86413f9330dc214da80b83fa959660ea3186deea3990cac404136", "_expires": "2027-02-03T19:41:20.000Z", "_created": "2026-10-26T19:35:17.000Z", "_published": "2026-10-26T19:41:22.988Z", "_upstream": "https://github.com/BiocStaging/MacrophageFramework", "_status": "success", "_maintainer": { "name": "Alessandro Palma", "email": "alessandro.palma2@uniroma1.it", "login": "alessandropalma-hub", "description": "", "uuid": 264351864, "orcid": "0000-0003-1300-5479" }, "_jobs": [ { "job": 121801696434, "time": 312, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "12682003020" }, { "job": 121801696441, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12681384494" }, { "job": 121801696432, "time": 321, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12682355895" }, { "job": 121801696576, "time": 140, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12681379395" }, { "job": 121801696483, "time": 150, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12681897901" }, { "job": 121798652992, "time": 353, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12680333531" }, { "job": 121801696424, "time": 243, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12681838313" }, { "job": 121801696548, "time": 120, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12681663733" }, { "job": 121801696572, "time": 128, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12680684024" }, { "job": 121801696553, "time": 314, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12680669007" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 4 }, "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471", "_commit": { "id": "34082803510846696ed9fb860eee3dd83ccdd629", "author": "AlessandroPalma-hub ", "committer": "GitHub ", "message": "Delete vignettes/data/GSE114725_demo.rds", "time": 1793027727 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "SeuratObject", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-41", "n": 3 }, { "week": "2026-42", "n": 6 }, { "week": "2026-43", "n": 10 }, { "week": "2026-44", "n": 12 } ], "_tags": [], "_topics": [ "geneexpression", "immunooncology", "singlecell", "software", "visualization" ], "_stars": 0, "_contributors": [ { "user": "alessandropalma-hub", "count": 31, "uuid": 264351864 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 2 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MacrophageFramework" }, "_devurl": "https://github.com/alessandropalma-hub/macrophageframework", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MacrophageFramework.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "analyze_macrophage_profile", "calculate_detection_coverage", "calculate_profile_similarity", "calculate_program_coherence", "load_ontology", "plot_macrophage_profile", "plot_macrophage_similarity", "plot_macrophage_umap", "score_programs", "summarize_macrophage_profile" ], "_help": [ { "page": "analyze_macrophage_profile", "title": "Analyze a macrophage expression profile", "topics": [ "analyze_macrophage_profile" ] }, { "page": "calculate_detection_coverage", "title": "Calculate program detection coverage", "topics": [ "calculate_detection_coverage" ] }, { "page": "calculate_profile_similarity", "title": "Calculate similarity between macrophage profiles", "topics": [ "calculate_profile_similarity" ] }, { "page": "calculate_program_coherence", "title": "Calculate program coherence", "topics": [ "calculate_program_coherence" ] }, { "page": "load_ontology", "title": "Load the macrophage ontology", "topics": [ "load_ontology" ] }, { "page": "plot_macrophage_profile", "title": "Plot multidimensional macrophage profiles", "topics": [ "plot_macrophage_profile" ] }, { "page": "plot_macrophage_similarity", "title": "Plot macrophage profile similarity", "topics": [ "plot_macrophage_similarity" ] }, { "page": "plot_macrophage_umap", "title": "Plot macrophage Framework annotations on a dimensional reduction", "topics": [ "plot_macrophage_umap" ] }, { "page": "score_programs", "title": "Score macrophage biological programs", "topics": [ "score_programs" ] }, { "page": "summarize_cluster_coherence", "title": "Summarize program coherence by cluster", "topics": [ "summarize_cluster_coherence" ] }, { "page": "summarize_macrophage_profile", "title": "Summarize macrophage profiles in a human-readable table", "topics": [ "summarize_macrophage_profile" ] } ], "_readme": "https://github.com/BiocStaging/MacrophageFramework/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "bitops", "bslib", "cachem", "caTools", "cli", "cluster", "codetools", "commonmark", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "deldir", "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", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "progressr", "promises", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppThread", "RcppTOML", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "Rtsne", "S7", "sass", "scales", "scattermore", "sctransform", "Seurat", "SeuratObject", "shiny", "sitmo", "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", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "MacrophageFramework.Rmd", "filename": "MacrophageFramework.html", "title": "A multidimensional framework for macrophage profiling with MacrophageFramework", "author": "Alessandro Palma", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Demonstration dataset", "Input and clustering", "Run MacrophageFramework", "Macrophage detection", "Manually specifying macrophage clusters", "Multidimensional program profiles", "Program intensity (score)", "Program coverage", "Program coherence", "Similarity between cluster profiles", "Visual summaries", "Original computational clusters", "Multidimensional framework annotation", "Program intensity", "Alternative input: expression matrix and cluster assignments", "Outputs and interpretation", "Reproducibility and limitations", "Session information" ], "created": "2026-10-14 20:05:31", "modified": "2026-10-25 15:35:16", "commits": 4 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "macrophageframework", "_universes": [ "biocstaging", "alessandropalma-hub" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-10-26T19:38:14.000Z", "distro": "resolute", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/28608731a76b5a012a06347480850fd8e413f1b639b8d8253ad1fd2f793d6d6e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.6.1", "os": "linux", "version": "0.99.0", "date": "2026-10-26T19:40:25.000Z", "distro": "resolute", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/72efc99cb3c4eee392d3102e4d1c32664343f3451aa1818cdac04466b152e548", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-10-26T19:37:51.000Z", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/11b0861087a7bd49e87e55a03b5167327c3b53dc36d14550c726efc8c246c0d7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.6.1", "os": "mac", "version": "0.99.0", "date": "2026-10-26T19:37:45.000Z", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/99ff7b55655918394c9eb9670308af951541d9945e764da58a20f4a1a1aed9fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-10-26T19:39:36.000Z", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/9660cf9acfbf5f5e9667a426e6af0e4da9d3c205d61f7ce1e722a40874128216", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-10-26T19:36:55.000Z", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/ca2aba766148a78a5768d7a034fc5224396bda4cca486fd9b496386d04a46630", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-10-26T19:37:05.000Z", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/90d6c209a68164419d1b03b5bb49f13feecb39da3cc64fbbba3909d3419db994", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" }, { "r": "4.6.1", "os": "win", "version": "0.99.0", "date": "2026-10-26T19:40:17.000Z", "commit": "34082803510846696ed9fb860eee3dd83ccdd629", "fileid": "https://r2.ropensci.org/ad725ad77b7edb127b552635a83c5a862ba6f33a6a445b46a67a73a41b924671", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/40387198471" } ] }