{ "_id": "6a1f2ca2b401979e734261ae", "Package": "CEMiTool", "Title": "Co-expression Modules identification Tool", "Version": "1.37.0", "Authors@R": "c( person(\"Pedro\", \"Russo\", email = \"pedro.russo@usp.br\",\nrole = c(\"aut\")), person(\"Gustavo\", \"Ferreira\", email =\n\"gustavo.rodrigues.ferreira@usp.br\", role = c(\"aut\")),\nperson(\"Matheus\", \"Bürger\", email =\"burger@usp.br\", role\n= c(\"aut\")), person(\"Lucas\", \"Cardozo\", email =\n\"lucas.cardozo@usp.br\", role = c(\"aut\")), person(\"Diogenes\", \"Lima\",\nemail = \"diogenes.lima@usp.br\", role = c(\"aut\")), person(\"Thiago\",\n\"Hirata\", email = \"thiago.hirata@usp.br\", role = c(\"aut\")),\nperson(\"Melissa\", \"Lever\", email = \"melissa.lever@usp.br\",\nrole = c(\"aut\")), person(\"Helder\", \"Nakaya\", email = \"hnakaya@usp.br\",\nrole = c(\"aut\", \"cre\")))", "Description": "The CEMiTool package unifies the discovery and the\nanalysis of coexpression gene modules in a fully automatic\nmanner, while providing a user-friendly html report with high\nquality graphs. Our tool evaluates if modules contain genes\nthat are over-represented by specific pathways or that are\naltered in a specific sample group. Additionally, CEMiTool is\nable to integrate transcriptomic data with interactome\ninformation, identifying the potential hubs on each network.", "License": "GPL-3", "Encoding": "UTF-8", "biocViews": "GeneExpression, Transcriptomics, GraphAndNetwork,\nmRNAMicroarray, RNASeq, Network, NetworkEnrichment, Pathways,\nImmunoOncology", "LazyData": "true", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:09 UTC", "RemoteUrl": "https://github.com/bioc/CEMiTool", "RemoteRef": "HEAD", "RemoteSha": "dffeb392d57fc0cc1a1aaca7168fc297e64457a6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-15 10:05:09 UTC", "User": "root" }, "Author": "Pedro Russo [aut],\nGustavo Ferreira [aut],\nMatheus Bürger [aut],\nLucas Cardozo [aut],\nDiogenes Lima [aut],\nThiago Hirata [aut],\nMelissa Lever [aut],\nHelder Nakaya [aut, cre]", "Maintainer": "Helder Nakaya ", "MD5sum": "19ad22b34f7c59ad5a3e442e6e3dbbd9", "_user": "bioc", "_type": "src", "_file": "CEMiTool_1.37.0.tar.gz", "_fileid": "d9d57d842d920ce89f2fe84de6f23cee3474ab03c17073734063b56da8399531", "_filesize": 5722268, "_sha256": "d9d57d842d920ce89f2fe84de6f23cee3474ab03c17073734063b56da8399531", "_created": "2026-05-15T10:05:09.000Z", "_published": "2026-06-02T19:18:58.172Z", "_jobs": [ { "job": 79152445454, "time": 249, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7014769166" }, { "job": 79152445338, "time": 423, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7014817756" }, { "job": 79152445468, "time": 424, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7014816518" }, { "job": 79152445380, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7014767628" }, { 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"fit_data", "title": "Retrieve scale-free model fit data", "topics": [ "fit_data", "fit_data,CEMiTool-method" ] }, { "page": "generate_report", "title": "CEMiTool report", "topics": [ "generate_report", "generate_report,CEMiTool-method" ] }, { "page": "get_adj", "title": "Calculate adjacency matrix", "topics": [ "get_adj", "get_adj,CEMiTool-method" ] }, { "page": "get_beta_data", "title": "Soft-threshold beta data", "topics": [ "get_beta_data", "get_beta_data,CEMiTool-method" ] }, { "page": "get_cemitool_r2_beta", "title": "Calculate CEMiTool beta and R2 values", "topics": [ "get_cemitool_r2_beta", "get_cemitool_r2_beta,CEMiTool-method" ] }, { "page": "get_connectivity", "title": "Calculate network connectivity", "topics": [ "get_connectivity", "get_connectivity,CEMiTool-method" ] }, { "page": "get_hubs", "title": "Get hubs", "topics": [ "get_hubs", "get_hubs,CEMiTool-method" ] }, { "page": "get_merged_mods", "title": "Merge similar modules", "topics": [ "get_merged_mods", 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