{ "_id": "6a1aeb5a1d7bb097a09f3ccb", "Package": "TBSignatureProfiler", "Title": "Profile RNA-Seq Data Using TB Pathway Signatures", "Version": "1.25.0", "Authors@R": "c(\nperson(\"Kiloni\", \"Quiles\", , \"kiloni.quiles@rutgers.edu\", role = c(\"cre\"),\ncomment = c(ORCID = \"0000-0002-7521-5255\")),\nperson(\"Aubrey R.\", \"Odom\", , \"aodom@bu.edu\", role = c(\"aut\", \"dtm\"),\ncomment = c(ORCID = \"0000-0001-7113-7598\")),\nperson(\"David\", \"Jenkins\", , \"dfj@bu.edu\", role = c(\"aut\", \"org\"),\ncomment = c(ORCID = \"0000-0002-7451-4288\")),\nperson(\"Xutao\", \"Wang\", , \"xutaow@bu.edu\", role = \"aut\"),\nperson(\"Yue\", \"Zhao\", , \"yuezh@bu.edu\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-5257-5103\")),\nperson(\"Christian\", \"Love\", , \"clove@bu.edu\", role = \"ctb\"),\nperson(\"W. Evan\", \"Johnson\", , \"wej@bu.edu\", role = \"aut\")\n)", "Description": "Gene signatures of TB progression, TB disease, and other\nTB disease states have been validated and published previously.\nThis package aggregates known signatures and provides\ncomputational tools to enlist their usage on other datasets.\nThe TBSignatureProfiler makes it easy to profile RNA-Seq data\nusing these signatures and includes common signature profiling\ntools including ASSIGN, GSVA, and ssGSEA. Original models for\nsome gene signatures are also available. A shiny app provides\nsome functionality alongside for detailed command line\naccessibility.", "License": "MIT + file LICENSE", "URL": "https://github.com/wejlab/TBSignatureProfiler,\nhttps://wejlab.github.io/TBSignatureProfiler-docs/", "BugReports": "https://github.com/wejlab/TBSignatureProfiler/issues", "VignetteBuilder": "knitr", "biocViews": "GeneExpression, DifferentialExpression", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "TRUE", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:35 UTC", "RemoteUrl": "https://github.com/bioc/TBSignatureProfiler", "RemoteRef": "HEAD", "RemoteSha": "3f57ba4f0c40662184264c03cc34753829462807", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:39:47 UTC", "User": "root" }, "Author": "Kiloni Quiles [cre] (ORCID: ),\nAubrey R. Odom [aut, dtm] (ORCID:\n),\nDavid Jenkins [aut, org] (ORCID:\n),\nXutao Wang [aut],\nYue Zhao [ctb] (ORCID: ),\nChristian Love [ctb],\nW. Evan Johnson [aut]", "Maintainer": "Kiloni Quiles ", "MD5sum": "5b87bdacb2bb4ec98b928e58ebfb17a5", "_user": "bioc", "_type": "src", "_file": "TBSignatureProfiler_1.25.0.tar.gz", "_fileid": "45944edf5e8d9fdb797ca8efc8de7ebd672a23f0f5851b2e1d330b42599bc81a", "_filesize": 3120407, "_sha256": "45944edf5e8d9fdb797ca8efc8de7ebd672a23f0f5851b2e1d330b42599bc81a", "_created": "2026-05-30T09:39:47.000Z", "_published": "2026-05-30T13:51:22.311Z", "_jobs": [ { "job": 78640240993, "time": 193, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307367256" }, { "job": 78640240997, "time": 347, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307381743" }, { "job": 78640241001, "time": 339, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307380823" }, { "job": 78640241002, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308641792" }, { "job": 78640240999, "time": 259, "config": 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"committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380755 }, "_maintainer": { "name": "Kiloni Quiles", "email": "kiloni.quiles@rutgers.edu", "login": "kiloni", "description": "Postdoctoral Associate | Rutgers New Jersey Medical School | Department of Medicine | Division of Infectious Diseases | Center for Emerging Pathogens", "uuid": 68908329, "orcid": "0000-0002-7521-5255" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "ASSIGN", "version": ">= 1.23.1", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "gdata", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "glmnet", "role": "Imports" 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"aubreyodom", "count": 409, "uuid": 25541738 }, { "user": "dfjenkins3", "count": 42, "uuid": 1692620 }, { "user": "cjlove1130", "count": 21, "uuid": 56614184 }, { "user": "xutao-wang", "count": 19, "uuid": 26095718 }, { "user": "jasonzhao0307", "count": 18, "uuid": 26149114 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "kiloni", "count": 10, "uuid": 68908329 }, { "user": "wevanjohnson", "count": 7, "uuid": 9968444 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 338, "source": "https://www.bioconductor.org/packages/stats/bioc/TBSignatureProfiler" }, "_mentions": 2, "_devurl": "https://github.com/wejlab/tbsignatureprofiler", "_pkgdown": "https://wejlab.github.io/TBSignatureProfiler-docs/", "_searchresults": 53, 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"title": "Bootstrap on Leave-one-out CV with Logistic Regression.", "topics": [ "Bootstrap_LOOCV_LR_AUC" ] }, { "page": "bootstrapAUC", "title": "Bootstrap the AUC and conduct T-Tests for a collection of signatures.", "topics": [ "bootstrapAUC" ] }, { "page": "common_sigAnnotData", "title": "Annotation information for published TB signatures.", "topics": [ "common_sigAnnotData" ] }, { "page": "compareAlgs", "title": "Compare scoring algorithms on a single signature via heatmap or boxplot.", "topics": [ "compareAlgs" ] }, { "page": "compareBoxplots", "title": "Create a comparison plot of boxplots for bootstrapped AUC values.", "topics": [ "compareBoxplots" ] }, { "page": "COVIDsignatures", "title": "A list of published/pre-print COVID-19 signatures.", "topics": [ "COVIDsignatures" ] }, { "page": "cv_glmnet_OriginalModel", "title": "Train original model for gene signatures Leong_24, Leong_RISK_29, Zhao_NANO_6 using lasso logistic regression.", "topics": [ "cv_glmnet_OriginalModel" ] }, { "page": "deseq2_norm_rle", "title": "Normalize gene expression count data.", "topics": [ "deseq2_norm_rle" ] }, { "page": "distinctColors", "title": "Generate a distinct palette for coloring different clusters.", "topics": [ "distinctColors" ] }, { "page": "evaluateOriginalModel", "title": "A function that implements the original methods for multiple TB signatures.", "topics": [ "evaluateOriginalModel" ] }, { "page": "knn_OriginalModel", "title": "Train original model for gene signatures Berry_393 and Berry_OD_86.", "topics": [ "knn_OriginalModel" ] }, { "page": "lda_OriginalModel", "title": "Train original model for gene signatures Jacobsen_3 and Sambarey_HIV_10.", "topics": [ "lda_OriginalModel" ] }, { "page": "LOOAUC_simple_multiple_noplot_one_df", "title": "Perform Leave-one-out CV with Logistic Regression.", "topics": [ "LOOAUC_simple_multiple_noplot_one_df" ] }, { "page": "mkAssay", "title": "Add SummarizedExperiment assays to the data structure.", "topics": [ "mkAssay" ] }, { "page": "ObtainSampleScore_OriginalModel", "title": "Obtain training data, testing data, and train signature's original model.", "topics": [ "ObtainSampleScore_OriginalModel" ] }, { "page": "OriginalTrainingData", "title": "Discovery datasets for corresponding gene signatures.", "topics": [ "OriginalTrainingData" ] }, { "page": "plotQuantitative", "title": "Create a boxplot using logistic regression and bootstrap LOOCV to evaluate signatures.", "topics": [ "plotQuantitative" ] }, { "page": "randomForest_OriginalModel", "title": "Train original model for gene signatures Maertzdorf_4, Maertzdorf_15, Verhagen_10, and LauxdaCosta_OD_3.", "topics": [ "randomForest_OriginalModel" ] }, { "page": "ref_combat_impute", "title": "A function for reference batch correction and imputation.", "topics": [ "ref_combat_impute" ] }, { "page": "runTBsigProfiler", "title": "Run TB gene signature profiling.", "topics": [ "runTBsigProfiler" ] }, { "page": "sigAnnotData", "title": "Annotation information for published TB signatures.", "topics": [ "sigAnnotData" ] }, { "page": "signatureBoxplot", "title": "Plot a boxplot of signature genes.", "topics": [ "signatureBoxplot" ] }, { "page": "signatureGeneHeatmap", "title": "Plot a heatmap of a single signature score with individual gene expression levels.", "topics": [ "signatureGeneHeatmap" ] }, { "page": "signatureHeatmap", "title": "Plot a heatmap of signature scores.", "topics": [ "signatureHeatmap" ] }, { "page": "SignatureQuantitative", "title": "Use logistic regression and bootstrap LOOCV to evaluate signatures.", "topics": [ "SignatureQuantitative" ] }, { "page": "signatureROCplot", "title": "Create an array of ROC plots to compare signatures.", "topics": [ "signatureROCplot" ] }, { "page": "signatureROCplot_CI", "title": "Create an array of ROC plots with confidence interval bands to compare signatures.", "topics": [ "signatureROCplot_CI" ] }, { "page": "subsetGeneSet", "title": "Filter gene expression value matrix based on certain 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