{ "_id": "6a1aa8bb1d7bb097a09d4c93", "Package": "RTNsurvival", "Type": "Package", "Title": "Survival analysis using transcriptional networks inferred by the\nRTN package", "Version": "1.37.0", "Author": "Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro", "Maintainer": "Clarice Groeneveld , Mauro A.\nA. Castro ", "Description": "RTNsurvival integrates regulons inferred by the RTN\npackage with survival data. For each regulon, a two-tailed GSEA\nframework computes a differential Enrichment Score (dES) at the\nindividual-sample level. The resulting dES distribution across\nsamples is then used to evaluate survival associations within\nthe cohort. Two primary workflows are supported: (i) Cox\nproportional hazards models, in which regulon activities are\ntreated as predictors of survival time, and (ii) Kaplan–Meier\nanalyses assessing cohort stratification based on regulon\nactivity. All graphical outputs are customizable according to\nuser specifications.", "License": "Artistic-2.0", "biocViews": "NetworkEnrichment, Survival, GeneRegulation,\nGeneSetEnrichment, NetworkInference, GraphAndNetwork", "LazyData": "TRUE", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:50 UTC", "RemoteUrl": "https://github.com/bioc/RTNsurvival", "RemoteRef": "HEAD", "RemoteSha": "0723cd1b710025755d3487c2ef805cdf45f281b4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 06:52:18 UTC", "User": "root" }, "MD5sum": "796548823cfc3c686d50edbe5b7068a7", "_user": "bioc", "_type": "src", "_file": "RTNsurvival_1.37.0.tar.gz", "_fileid": "53046569205008ba5bb07fb6f0bbe3558376aceacfd7ac67408d0a53b2788590", "_filesize": 708184, "_sha256": "53046569205008ba5bb07fb6f0bbe3558376aceacfd7ac67408d0a53b2788590", "_created": "2026-05-30T06:52:18.000Z", "_published": "2026-05-30T09:07:07.546Z", "_jobs": [ { "job": 78631580958, "time": 153, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306241841" }, { "job": 78631580966, "time": 353, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306263661" }, { "job": 78631580973, "time": 330, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306261151" }, { "job": 78631580974, "time": 240, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307055603" }, { "job": 78631580959, "time": 215, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307053479" }, { "job": 78631337769, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306226059" }, { "job": 78631580950, "time": 169, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306243463" }, { "job": 78631580972, "time": 254, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306252865" }, { "job": 78631580971, "time": 249, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306252276" }, { "job": 78631580969, "time": 242, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306251469" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 17 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677271888", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RTNsurvival", "_commit": { "id": "0723cd1b710025755d3487c2ef805cdf45f281b4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380350 }, "_maintainer": { "name": "Clarice Groeneveld", "email": "mauro.a.castro@gmail.com", "login": "csgroen", "description": "Director of Cordeliers Artificial Intelligence and Bioinformatics Core Facility\n//\nPhD from PSL Research University and Institute Curie", "uuid": 17986920 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "RTN", "version": ">= 2.32", "role": "Depends" }, { "package": "RTNduals", "version": ">= 1.32", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "survival", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "egg", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "dunn.test", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-08", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "networkenrichment", "survival", "generegulation", "genesetenrichment", "networkinference", "graphandnetwork" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 384, "source": "https://www.bioconductor.org/packages/stats/bioc/RTNsurvival" }, "_mentions": 1, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/RTNsurvival.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "hclust_semisupervised", "tni2tnsPreprocess", "tnsAREA3", "tnsCox", "tnsCoxInteraction", "tnsGet", "tnsGSEA2", "tnsInteraction", "tnsKM", "tnsKmInteraction", "tnsPlotCovariates", "tnsPlotCox", "tnsPlotCoxInteraction", "tnsPlotGSEA2", "tnsPlotKM", "tnsPlotKmInteraction", "tnsPlotSRE", "tnsSRD", "tnsSRE", "tnsStratification" ], "_datasets": [ { "name": "survival.data", "title": "A pre-processed dataset for demonstration purposes only.", "object": "survival.data", "class": [ "data.frame" ], "fields": [ "time", "event", "Grade", "Size", "LN", "Age", "ER+", "ER-", "PR+", "PR-", "LumA", "LumB", "Basal", "Her2", "Normal", "G1", "G2", "G3", "HT" ], "rows": 200, "table": true, "tojson": true } ], "_help": [ { "page": "RTNsurvival-package", "title": "Performs survival analysis using transcriptional networks inferred by the RTN package.", "topics": [ "RTNsurvival-package", "RTNsurvival" ] }, { "page": "hclust_semisupervised", "title": "Semi-supervised hierarchical clustering", "topics": [ "hclust_semisupervised" ] }, { "page": "tni2tnsPreprocess-methods", "title": "Preprocessing of TNS class objects", "topics": [ "tni2tnsPreprocess", "tni2tnsPreprocess,TNI-method" ] }, { "page": "TNS-class", "title": "TNS: An S4 class for survival analysis using transcriptional networks inferred by the RTN package.", "topics": [ "TNS", "TNS-class" ] }, { "page": "TNS.data", "title": "A pre-processed dataset for demonstration purposes only.", "topics": [ "survival.data" ] }, { "page": "tnsAREA3-methods", "title": "Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm", "topics": [ "tnsAREA3", "tnsAREA3,TNS-method" ] }, { "page": "tnsCox-methods", "title": "Cox regression analysis for TNS class objects", "topics": [ "tnsCox", "tnsCox,TNS-method" ] }, { "page": "tnsCoxInteraction-methods", "title": "Cox regression analysis for dual regulons", "topics": [ "tnsCoxInteraction", "tnsCoxInteraction,TNS-method" ] }, { "page": "tnsGet-methods", "title": "Get information from slots in a TNS object", "topics": [ "tnsGet", "tnsGet,TNS-method" ] }, { "page": "tnsGSEA2-methods", "title": "Compute regulon activity using 2-tailed Gene Set Enrichment Analysis", "topics": [ "tnsGSEA2", "tnsGSEA2,TNS-method" ] }, { "page": "tnsInteraction-methods", "title": "Survival analysis for dual regulons", "topics": [ "tnsInteraction", "tnsInteraction,TNS-method" ] }, { "page": "tnsKM-methods", "title": "Kaplan-Meier analysis for TNS class objects", "topics": [ "tnsKM", "tnsKM,TNS-method" ] }, { "page": "tnsKmInteraction-methods", "title": "Kaplan-Meier analysis for dual regulons", "topics": [ "tnsKmInteraction", "tnsKmInteraction,TNS-method" ] }, { "page": "tnsPlotCovariates-methods", "title": "Plot regulon activity and categorical covariates", "topics": [ "tnsPlotCovariates", "tnsPlotCovariates,TNS-method" ] }, { "page": "tnsPlotCox-methods", "title": "Cox plots for TNS class objects", "topics": [ "tnsPlotCox", "tnsPlotCox,TNS-method" ] }, { "page": "tnsPlotCoxInteraction-methods", "title": "Plot results from Cox regression analysis for dual regulons", "topics": [ "tnsPlotCoxInteraction", "tnsPlotCoxInteraction,TNS-method" ] }, { "page": "tnsPlotGSEA2-methods", "title": "Plot 2-tailed GSEA for a sample from a TNS", "topics": [ "tnsPlotGSEA2", "tnsPlotGSEA2,TNS-method" ] }, { "page": "tnsPlotKM-methods", "title": "Kaplan-Meier plots for TNS class objects", "topics": [ "tnsPlotKM", "tnsPlotKM,TNS-method" ] }, { "page": "tnsPlotKmInteraction-methods", "title": "Plot results from Kaplan-Meier analysis for dual regulons", "topics": [ "tnsPlotKmInteraction", "tnsPlotKmInteraction,TNS-method" ] }, { "page": "tnsPlotSRE-methods", "title": "Plot Subgroup Regulon Enrichment for TNS-class objects", "topics": [ "tnsPlotSRE", "tnsPlotSRE,TNS-method" ] }, { "page": "tnsSRD-methods", "title": "Subgroup Regulon Difference for TNS-class objects", "topics": [ "tnsSRD", "tnsSRD,TNS-method" ] }, { "page": "tnsSRE-methods", "title": "Subgroup Regulon Enrichment for TNS-class objects", "topics": [ "tnsSRE", "tnsSRE,TNS-method" ] }, { "page": "tnsStratification", "title": "Sample stratification for a TNS object", "topics": [ "tnsStratification" ] } ], "_rundeps": [ "abind", "askpass", "backports", "base64enc", "Biobase", "BiocGenerics", "boot", "broom", "bslib", "ca", "cachem", "car", "carData", "class", "cli", "cluster", "codetools", "colorspace", "corrr", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "Deriv", "digest", "doBy", "dplyr", "dunn.test", "e1071", "egg", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "forecast", "Formula", "fracdiff", "fs", "gclus", "generics", "GenomicRanges", "ggplot2", "ggrepel", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "infotheo", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "limma", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minet", "minqa", "mixtools", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "otel", "pbkrtest", "permute", "pheatmap", "pillar", "pkgconfig", "plotly", "promises", "proxy", "purrr", "pwr", "qap", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "RedeR", "reformulas", "registry", "rlang", "rmarkdown", "RTN", "RTNduals", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scrutiny", "segmented", "Seqinfo", "seriation", "snow", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "TSP", "urca", "utf8", "vctrs", "vegan", "viper", "viridisLite", "withr", "xfun", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "RTNsurvival.Rmd", "filename": "RTNsurvival.html", "title": "RTNsurvival: multivariate survival analysis using transcriptional networks and regulons.", "author": "Clarice S Groeneveld, Vinícius S Chagas, Gordon Robertson, Kerstin B Meyer, Mauro AA Castro.", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Quick Start", "Load regulons and survival data", "Preprocess input data", "Compute regulon activity", "Run the Cox analysis pipeline", "Run the Kaplan-Meier analysis pipeline", "Plot 2-tailed GSEA for individual samples", "Plot regulon activity for all samples", "Session information", "References" ], "created": "2017-02-02 21:34:46", "modified": "2025-07-23 18:55:28", "commits": 24 } ], "_score": 3.778151250383644, "_indexed": true, "_nocasepkg": "rtnsurvival", "_universes": [ "bioc", "csgroen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-04-30T15:47:02.000Z", "distro": "noble", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "273fa284245ba2419a7b99b93b6fa5b9fa7f6a30efce4b172f2ca226e4198f80", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.6.0", "os": "linux", "version": "1.37.0", "date": "2026-04-30T15:47:15.000Z", "distro": "noble", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "baa4d1d52eac0bfd0b6547cd64edf658be10a27912b282bd58c516779c43284d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-04-30T17:20:58.000Z", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "e0ecca926f330354d6d59d8bac24f53bca19a0e21bedb8fda84b89264f082efc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.6.0", "os": "mac", "version": "1.37.0", "date": "2026-04-30T17:20:51.000Z", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "619ac616a1eaa671fe9061eeaf9b7ed5ef07856053024cea2f6da1613cb5c9d8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-04-30T15:45:44.000Z", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "93566125ad874c229df54da65e337d36578214b68d40b29204df308f48d89d1e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-04-30T15:45:28.000Z", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "cb4bfd4cf25a4bd8a8f979557fc217a504c2dd09baaaff780b7a6fff67986484", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.6.0", "os": "win", "version": "1.37.0", "date": "2026-04-30T15:46:21.000Z", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "2b6b7ae0907cfd33d60924f421f710e760c767f9da08b5ac44759e309f0b61fe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-05-22T21:03:28.000Z", "commit": "0723cd1b710025755d3487c2ef805cdf45f281b4", "fileid": "4db56b26fd7de4ac82ad992f6b5157dbbced8c48c37d98dc4f2d5da18bb3d89e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173821447" } ] }