{ "_id": "6a226e98cd65a98ecbd47c80", "Package": "lncRna", "Title": "A Comprehensive Workflow for Long Non-coding RNA Identification\nand Functional Analysis", "Version": "1.1.0", "Authors@R": "c(\nperson(given = \"Jan Pawel\",\nfamily = \"Jastrzebski\",\nrole = c(\"aut\", \"cre\"),\nemail = \"bioinformatyka@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8699-7742\")),\nperson(given = \"Damian\",\nfamily = \"Czopek\",\nrole = c(\"ctb\", \"aut\"),\nemail = \"dcwmpl@gmail.com\",\ncomment = c(ORCID = \"0009-0005-3471-4866\")),\nperson(given = \"Mariusz\",\nfamily = \"Jankowski\",\nrole = c(\"ctb\"),\nemail = \"ma.jankowski99@gmail.com\",\ncomment = c(ORCID = \"0009-0000-7872-4023\")),\nperson(given = \"Monika\",\nfamily = \"Gawronska\",\nrole = c(\"ctb\"),\nemail = \"gawronska572@gmail.com\",\ncomment = c(ORCID = \"0009-0001-2677-6371\")),\nperson(given = \"Wiktor\",\nfamily = \"Babis\",\nrole = c(\"ctb\"),\nemail = \"wiktorbabis@gmail.com\",\ncomment = c(ORCID = \"0009-0006-3648-3413\")),\nperson(given = \"Stefano\",\nfamily = \"Pascarella\",\nrole = c(\"ctb\"),\nemail = \"stefano.pascarella@uniroma1.it\",\ncomment = c(ORCID = \"0000-0002-6822-4022\")),\nperson(\"Hugo\", \"Gruson\", ,\n\"hugo.gruson+R@normalesup.org\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-4094-1476\"))\n)", "Description": "Provides a complete workflow for the identification,\nanalysis, and functional annotation of long non-coding RNAs\n(lncRNAs) from RNA-Seq data. The package includes functions for\nfiltering transcripts from GTF files, evaluating the\nperformance of multiple coding potential prediction tools\n(e.g., CPC2, PLEK, CPAT), and summarizing their agreement. It\nenables systematic performance analysis of individual tools,\n\"at least N\" tool consensus, and all possible tool\ncombinations. Functional analysis is supported through the\nidentification of potential cis- and trans-acting interactions\nwith protein-coding genes, followed by enrichment analysis.\nResults can be visualized using a variety of plots, including\nradar plots, clock plots, and interactive Sankey diagrams.", "License": "MIT + file LICENSE", "URL": "https://github.com/prodakt/lncRna", "BugReports": "https://github.com/prodakt/lncRna/issues", "biocViews": "Software, GeneExpression, RNASeq, Transcription,\nVisualization, QualityControl, FunctionalGenomics,\nClassification, FunctionalPrediction", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:07:14 UTC", "RemoteUrl": "https://github.com/bioc/lncRna", "RemoteRef": "HEAD", "RemoteSha": 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