{ "_id": "6a1be7411d7bb097a0a1ae7c", "Package": "BloodGen3Module", "Type": "Package", "Title": "This R package for performing module repertoire analyses and\ngenerating fingerprint representations", "Version": "1.21.0", "Date": "2020-11-05", "Authors@R": "person(given = \"Darawan\",\nfamily = \"Rinchai\",\nrole = c(\"aut\", \"cre\"),\nemail = \"drinchai@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8851-7730\"))", "Description": "The BloodGen3Module package provides functions for R user\nperforming module repertoire analyses and generating\nfingerprint representations. Functions can perform group\ncomparison or individual sample analysis and visualization by\nfingerprint grid plot or fingerprint heatmap. Module repertoire\nanalyses typically involve determining the percentage of the\nconstitutive genes for each module that are significantly\nincreased or decreased. As we describe in\ndetails;https://www.biorxiv.org/content/10.1101/525709v2 and\nhttps://pubmed.ncbi.nlm.nih.gov/33624743/, the results of\nmodule repertoire analyses can be represented in a fingerprint\nformat, where red and blue spots indicate increases or\ndecreases in module activity. These spots are subsequently\nrepresented either on a grid, with each position being assigned\nto a given module, or in a heatmap where the samples are\narranged in columns and the modules in rows.", "License": "GPL-2", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "biocViews": "Software, Visualization, GeneExpression", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev perl libnode-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:07 UTC", "RemoteUrl": "https://github.com/bioc/BloodGen3Module", "RemoteRef": "HEAD", "RemoteSha": "d300177ee9265d66b21705dafd7928c37ea57739", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:41:14 UTC", "User": "root" }, "Author": "Darawan Rinchai [aut, cre] (ORCID:\n)", "Maintainer": "Darawan Rinchai ", "MD5sum": "fc3b7a8655aec393f2fd62e5b2803ea4", "_user": "bioc", "_type": "src", "_file": 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1777380967 }, "_maintainer": { "name": "Darawan Rinchai", "email": "drinchai@gmail.com", "login": "darinchai", "description": "", "uuid": 150455475, "orcid": "0000-0001-8851-7730" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "ExperimentHub", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "testthat", "role": "Imports" }, { "package": "ComplexHeatmap", "version": ">= 1.99.8", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": 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"https://www.bioconductor.org/packages/stats/bioc/BloodGen3Module" }, "_mentions": 2, "_searchresults": 14, "_rbuild": "4.6.0", "_assets": [ "extra/BloodGen3Module.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "fingerprintplot", "fold_change", "gridplot", "Groupcomparison", "Groupcomparisonlimma", "Individualcomparison" ], "_help": [ { "page": "color", "title": "Color for fingerprint visulization", "topics": [ "color" ] }, { "page": "fingerprintplot", "title": "Individual fingerprint visualization The fingerprintplot function will generate fingerprint heatmap plots as a pdf file. The file will be saved in the working directory specified for the analysis. The default cut off for visualization is set at 15%, it can be changed to any value between 0-100%.", "topics": [ "fingerprintplot" ] }, { "page": "fold_change", "title": "calculation of Fold-Change", "topics": [ "fold_change" ] }, { "page": "Gen3_ann", "title": "Functional annotation for visulization", "topics": [ "Gen3_ann" ] }, { "page": "gridplot", "title": "Fingerprint grid visualization", "topics": [ "gridplot" ] }, { "page": "Groupcomparison", "title": "Group comparison analysis", "topics": [ "Groupcomparison" ] }, { "page": "Groupcomparisonlimma", "title": "Group comparison analysis using limma", "topics": [ "Groupcomparisonlimma" ] }, { "page": "Individualcomparison", "title": "Individual single sample analysis", "topics": [ "Individualcomparison" ] }, { "page": "Module_listGen3", "title": "Module identifer and list membership in each module", "topics": [ "Module_listGen3" ] } ], "_readme": "https://github.com/bioc/BloodGen3Module/raw/HEAD/README.md", "_rundeps": [ "abind", 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