{ "_id": "6a1aa9341d7bb097a09d4ce4", "Package": "RTN", "Type": "Package", "Title": "RTN: Reconstruction of Transcriptional regulatory Networks and\nanalysis of regulons", "Version": "2.37.0", "Author": "Clarice Groeneveld [ctb], Gordon Robertson [ctb], Xin Wang\n[aut], Michael Fletcher [aut], Florian Markowetz [aut], Kerstin\nMeyer [aut], and Mauro Castro [aut]", "Maintainer": "Mauro Castro ", "Description": "A transcriptional regulatory network (TRN) consists of a\ncollection of transcription factors (TFs) and the regulated\ntarget genes. TFs are regulators that recognize specific DNA\nsequences and guide the expression of the genome, either\nactivating or repressing the expression the target genes. The\nset of genes controlled by the same TF forms a regulon. This\npackage provides classes and methods for the reconstruction of\nTRNs and analysis of regulons.", "License": "Artistic-2.0", "biocViews": "Transcription, Network, NetworkInference, NetworkEnrichment,\nGeneRegulation, GeneExpression, GraphAndNetwork,\nGeneSetEnrichment, GeneticVariability", "VignetteBuilder": "knitr", "URL": "http://dx.doi.org/10.1038/ncomms3464", "Collate": "ClassUnions.R AllChecks.R AllClasses.R AllGenerics.R\nAllSupplementsTNA.R AllSupplementsTNI.R AllSupplementsAVS.R\nAllPlotsTNA.R AllPlotsAVS.R AllPlotsTNI.R TNA-methods.R\nTNI-methods.R AVS-methods.R TNI-pruning.R TNI-annotation.R\nTNI-subgroups.R", "LazyLoad": "yes", "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 12:38:01 UTC", "RemoteUrl": "https://github.com/bioc/RTN", "RemoteRef": "HEAD", "RemoteSha": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 06:53:02 UTC", "User": "root" }, "MD5sum": "4ae40c55ec375d6a455881309c1d4a75", "_user": "bioc", "_type": "src", "_file": "RTN_2.37.0.tar.gz", "_fileid": "fac64623efb1d4276f8142cb03c5b69acf4590eb146d32e5c1f1c550f47aa198", "_filesize": 10819865, "_sha256": "fac64623efb1d4276f8142cb03c5b69acf4590eb146d32e5c1f1c550f47aa198", "_created": "2026-05-30T06:53:02.000Z", "_published": "2026-05-30T09:09:08.643Z", "_jobs": [ { "job": 78631625569, "time": 217, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306254237" }, { "job": 78631625578, "time": 389, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306273349" }, { "job": 78631625574, "time": 346, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306268660" }, { "job": 78631625580, "time": 252, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307061745" }, { "job": 78631625585, "time": 254, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307061845" }, { "job": 78631334400, "time": 341, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306230786" }, { "job": 78631625575, "time": 163, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306247945" }, { "job": 78631625591, "time": 683, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306308911" }, { "job": 78631625593, "time": 608, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306300016" }, { "job": 78631625588, "time": 288, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306261875" } ], "_bioccheck": { "error": 2, "warning": 3, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677268894", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RTN", "_commit": { "id": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379881 }, "_maintainer": { "name": "Mauro Castro", "email": "mauro.a.castro@gmail.com", "login": "castromaa", "description": "", "uuid": 11091083 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.3", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "RedeR", "role": "Imports" }, { "package": "minet", "role": "Imports" }, { "package": "viper", "role": "Imports" }, { "package": "mixtools", "role": "Imports" }, { "package": "snow", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "car", "role": "Imports" }, { "package": "pwr", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-08", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.37.0", "bioc": "3.24" }, { "branch": "release", "version": "2.36.0", "bioc": "3.23" } ], "_topics": [ "transcription", "network", "networkinference", "networkenrichment", "generegulation", "geneexpression", "graphandnetwork", "genesetenrichment", "geneticvariability" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 630, "source": "https://www.bioconductor.org/packages/stats/bioc/RTN" }, "_mentions": 17, "_searchresults": 90, "_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/RTN.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "avs.evse", "avs.get", "avs.pevse", "avs.plot1", "avs.plot2", "avs.rvse", "avs.vse", "tna.get", "tna.gsea1", "tna.gsea2", "tna.mra", "tna.plot.gsea1", "tna.plot.gsea2", "tni.alpha.adjust", "tni.annotate.regulons", "tni.annotate.samples", "tni.area3", "tni.bootstrap", "tni.conditional", "tni.constructor", "tni.dpi.filter", "tni.get", "tni.graph", "tni.gsea2", "tni.overlap.genesets", "tni.permutation", "tni.plot.checks", "tni.plot.sre", "tni.preprocess", "tni.prune", "tni.regulon.summary", "tni.replace.samples", "tni.sre", "tni2tna.preprocess", "upgradeTNA", "upgradeTNI" ], "_datasets": [ { "name": "pksData", "title": "Pre-processed datasets for the RTN package.", "object": "pksData", "file": "pksData.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "stni", "title": "A pre-processed TNI for demonstration purposes only.", "object": "stni", "file": "stni.RData", "class": [ "TNI" ], "fields": [], "table": false, "tojson": false }, { "name": "tfsData", "title": "Pre-processed datasets for the RTN package.", "object": "tfsData", "file": "tfsData.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "tnaData", "title": "Pre-processed datasets for the RTN package.", "object": "tnaData", "file": "tnaData.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "tniData", "title": "Pre-processed datasets for the RTN package.", "object": "tniData", "file": "tniData.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "RTN-package", "title": "Reconstruction and Analysis of Transcriptional Networks.", "topics": [ "RTN-package", "RTN" ] }, { "page": "AVS-class", "title": "Class '\"AVS\"': an S4 class for variant set enrichment analysis.", "topics": [ "AVS-class", "avs.evse,AVS-method", "avs.get,AVS-method", "avs.pevse,AVS-method", "avs.rvse,AVS-method", "avs.vse,AVS-method" ] }, { "page": "avs.evse", "title": "An eQTL/VSE pipeline for variant set enrichment analysis.", "topics": [ "avs.evse" ] }, { "page": "avs.get", "title": "Get information from individual slots in an AVS object.", "topics": [ "avs.get" ] }, { "page": "avs.pevse", "title": "An EVSE pipeline using precomputed eQTLs.", "topics": [ "avs.pevse" ] }, { "page": "avs.plot1", "title": "Plot results from AVS methods, single plots.", "topics": [ "avs.plot1" ] }, { "page": "avs.plot2", "title": "Plot results from AVS methods, multiple plots.", "topics": [ "avs.plot2" ] }, { "page": "avs.rvse", "title": "An rQTL/VSE pipeline for variant set enrichment analysis.", "topics": [ "avs.rvse" ] }, { "page": "avs.vse", "title": "Variant set enrichment (VSE) analysis.", "topics": [ "avs.vse" ] }, { "page": "RTN.data", "title": "Pre-processed datasets for the RTN package.", "topics": [ "pksData", "tfsData", "tnaData", "tniData" ] }, { "page": "TNA-class", "title": "Class '\"TNA\"': an S4 class for Transcriptional Network Analysis.", "topics": [ "TNA-class", "tna.get,TNA-method", "tna.gsea1,TNA-method", "tna.gsea2,TNA-method", "tna.mra,TNA-method" ] }, { "page": "tna.get", "title": "Get information from individual slots in a TNA object.", "topics": [ "tna.get" ] }, { "page": "tna.gsea1", "title": "One-tailed Gene Set Enrichment Analysis (GSEA) over a list of regulons.", "topics": [ "tna.gsea1" ] }, { "page": "tna.gsea2", "title": "Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of regulons.", "topics": [ "tna.gsea2" ] }, { "page": "tna.mra", "title": "Master Regulator Analysis (MRA) over a list of regulons.", "topics": [ "tna.mra" ] }, { "page": "tna.plot.gsea1", "title": "Plot enrichment analyses from TNA objects.", "topics": [ "tna.plot.gsea1" ] }, { "page": "tna.plot.gsea2", "title": "Plot enrichment analyses from TNA objects.", "topics": [ "tna.plot.gsea2" ] }, { "page": "TNI-class", "title": "Class '\"TNI\"': an S4 class for Transcriptional Network Inference.", "topics": [ "TNI-class", "tni.annotate.regulons,TNI-method", "tni.annotate.samples,TNI-method", "tni.area3,TNI-method", "tni.bootstrap,TNI-method", "tni.conditional,TNI-method", "tni.dpi.filter,TNI-method", "tni.get,TNI-method", "tni.graph,TNI-method", "tni.gsea2,TNI-method", "tni.overlap.genesets,TNI-method", "tni.permutation,TNI-method", "tni.preprocess,TNI-method", "tni.prune,TNI-method", "tni.regulon.summary,TNI-method", "tni.replace.samples,TNI-method", "tni.sre,TNI-method", "tni2tna.preprocess,TNI-method" ] }, { "page": "tni.alpha.adjust", "title": "Adjust the significance level for two datasets.", "topics": [ "tni.alpha.adjust" ] }, { "page": "tni.annotate.regulons", "title": "Annotate regulons with external gene set collections.", "topics": [ "tni.annotate.regulons" ] }, { "page": "tni.annotate.samples", "title": "Annotate samples with external gene set collections.", "topics": [ "tni.annotate.samples" ] }, { "page": "tni.area3", "title": "Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm", "topics": [ "tni.area3" ] }, { "page": "tni.bootstrap", "title": "Inference of consensus transcriptional networks.", "topics": [ "tni.bootstrap" ] }, { "page": "tni.conditional", "title": "Modulators of transcription factor (TF) activity assessed by conditional mutual information analysis.", "topics": [ "tni.conditional" ] }, { "page": "tni.constructor", "title": "A constructor for objects of class TNI.", "topics": [ "tni.constructor" ] }, { "page": "TNI.data", "title": "A pre-processed TNI for demonstration purposes only.", "topics": [ "stni" ] }, { "page": "tni.dpi.filter", "title": "Data Processing Inequality (DPI) filter.", "topics": [ "tni.dpi.filter" ] }, { "page": "tni.get", "title": "Get information from individual slots in a TNI object.", "topics": [ "tni.get" ] }, { "page": "tni.graph", "title": "Compute a graph from TNI objects (Deprecated).", "topics": [ "tni.graph" ] }, { "page": "tni.gsea2", "title": "Compute regulon activity by calling GSEA2 (two-tailed Gene Set Enrichment Analysis) algorithm", "topics": [ "tni.gsea2" ] }, { "page": "tni.overlap.genesets", "title": "Associate regulons with external gene set collections.", "topics": [ "tni.overlap.genesets" ] }, { "page": "tni.permutation", "title": "Inference of transcriptional networks.", "topics": [ "tni.permutation" ] }, { "page": "tni.plot.checks", "title": "Plot regulon target counts.", "topics": [ "tni.plot.checks" ] }, { "page": "tni.plot.sre", "title": "Plot Subgroup Regulon Enrichment for TNI-class objects.", "topics": [ "tni.plot.sre" ] }, { "page": "tni.preprocess", "title": "A preprocessing function for objects of class TNI.", "topics": [ "tni.preprocess" ] }, { "page": "tni.prune", "title": "Prune regulons to remove redundant targets for regulon activity analysis", "topics": [ "tni.prune" ] }, { "page": "tni.regulon.summary", "title": "Summary of regulon characteristics.", "topics": [ "tni.regulon.summary" ] }, { "page": "tni.replace.samples", "title": "Entry point to assess new samples with previously calculated regulons.", "topics": [ "tni.replace.samples" ] }, { "page": "tni.sre", "title": "Subgroup Regulon Enrichment for TNI-class objects.", "topics": [ "tni.sre" ] }, { "page": "tni2tna.preprocess", "title": "A preprocessing function for objects of class TNI.", "topics": [ "tni2tna.preprocess" ] }, { "page": "upgradeTNA", "title": "Upgrade objects of class TNI.", "topics": [ "upgradeTNA" ] }, { "page": "upgradeTNI", "title": "Upgrade objects of class TNI.", "topics": [ "upgradeTNI" ] } ], "_rundeps": [ "abind", "askpass", "backports", "base64enc", "Biobase", "BiocGenerics", "boot", "broom", "bslib", "cachem", "car", "carData", "class", "cli", "colorspace", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "Deriv", "digest", "doBy", "dplyr", "e1071", "evaluate", "farver", "fastmap", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "infotheo", "IRanges", "isoband", "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", "pheatmap", "pillar", "pkgconfig", "plotly", "promises", "proxy", "purrr", "pwr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "RedeR", "reformulas", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "segmented", "Seqinfo", "snow", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "viper", "viridisLite", "withr", "xfun", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "RTN.Rmd", "filename": "RTN.html", "title": "RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons.", "author": "Clarice Groeneveld [ctb], Gordon Robertson [ctb], Xin Wang [aut], Michael Fletcher [aut], Florian Markowetz [aut], Kerstin Meyer [aut], and Mauro Castro [aut].", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Quick Start", "Transcriptional Network Inference (TNI)", "Transcriptional Network Analysis (TNA)", "TCGA-BRCA case study", "Context", "Package and data requirements", "Data preprocessing", "Inferring the transcriptional regulatory network", "How to select the significance level when inferring regulons from different cohorts", "METABRIC case study", "Regulon activity profiles", "Assessing samples with regulons calculated from a different cohort", "Citation", "Session information", "References" ], "created": "2017-09-29 17:09:21", "modified": "2023-11-23 19:09:40", "commits": 19 } ], "_score": 6.209515014542631, "_indexed": true, "_nocasepkg": "rtn", "_universes": [ "bioc", "castromaa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.37.0", "date": "2026-04-30T15:46:22.000Z", "distro": "noble", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "e53b2612fad1fb5bf3e558050454329c09f285deea13891d979427c887ecd3f2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.6.0", "os": "linux", "version": "2.37.0", "date": "2026-04-30T15:46:37.000Z", "distro": "noble", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "09715bcd23e416dc76fc414c794643926b493cf08c213c8f0f77e2569c5b4b95", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.5.3", "os": "mac", "version": "2.37.0", "date": "2026-04-30T17:20:47.000Z", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "581742ed215cd3323735c24fd7730e0084e613242bec55ddb8d4b321deabb998", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.6.0", "os": "mac", "version": "2.37.0", "date": "2026-04-30T17:20:43.000Z", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "131211e028d0b968c48650bb35d8ec8ffa20642769030c9136211dea8a6af153", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.7.0", "os": "win", "version": "2.37.0", "date": "2026-04-30T15:45:18.000Z", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "4973beac11d1ecaf4dac9f639d8550580159396947b772aa889f1c463dd615b0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.5.3", "os": "win", "version": "2.37.0", "date": "2026-04-30T15:49:26.000Z", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "dbb28d277307b4ecdce47c9595f1b4a7aa8797ace46c55cd95debcb234ffa7c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.6.0", "os": "win", "version": "2.37.0", "date": "2026-04-30T15:47:55.000Z", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "0899385053f00ee2b33d2f597e352701429671d2f726d5f9f741318fc3955183", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" }, { "r": "4.6.0", "os": "wasm", "version": "2.37.0", "date": "2026-05-22T21:03:31.000Z", "commit": "8d8eb9db7576c7c9a802f4faed7ec0745dcac871", "fileid": "5969a58d5fa5635a8524be7411453b4574c9e1cd900e128f0dc6bd49a25cb1c9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25173814998" } ] }