{ "_id": "6a1022a3acfb0bcc41c8ccdc", "Package": "DuplexDiscovereR", "Title": "Analysis of the data from RNA duplex probing experiments", "Authors@R": "c(person(\"Egor\", \"Semenchenko\", ,\nemail = \"yegor.smb@gmail.com\",\nrole = c(\"aut\", \"cre\",\"cph\"),\ncomment = c(ORCID = \"0009-0007-5306-076X\")),\nperson(\"Volodymyr\", \"Tsybulskyi\", ,\nemail = \"Volodymyr.Tsybulskyi@mdc-berlin.de\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0002-4141-6291\")),\nperson(\"Irmtraud M.\", \"Meyer\", ,\nemail = \"irmtraud.m.meyer@cantab.net\", role = c(\"aut\",\"cph\"),\ncomment = c(ORCID = \"0000-0002-4048-3479\")))", "Description": "DuplexDiscovereR is a package designed for analyzing data\nfrom RNA cross-linking and proximity ligation protocols such as\nSPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts\ninput in the form of chimerically or split-aligned reads. It\nincludes procedures for alignment classification, filtering,\nand efficient clustering of individual chimeric reads into\nduplex groups (DGs). Once DGs are identified, the package\npredicts RNA duplex formation and their hybridization energies.\nAdditional metrics, such as p-values for random ligation\nhypothesis or mean DG alignment scores, can be calculated to\nrank final set of RNA duplexes. Data from multiple experiments\nor replicates can be processed separately and further compared\nto check the reproducibility of the experimental method.", "License": "GPL-3", "URL": "https://github.com/Egors01/DuplexDiscovereR/", "BugReports": "https://github.com/Egors01/DuplexDiscovereR/issues/", "Encoding": "UTF-8", "NeedsCompilation": "no", "Version": "1.7.0", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "BiocType": "Software", "biocViews": "Sequencing, Transcriptomics, StructuralPrediction,\nClustering, SplicedAlignment", "LazyData": "false", "VignetteBuilder": "knitr", "VignetteEngine": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:52 UTC", "RemoteUrl": "https://github.com/bioc/DuplexDiscovereR", "RemoteRef": "HEAD", "RemoteSha": "7fa11a7479b775d0f76b1c1187ed3713854b5a1d", "Packaged": { "Date": "2026-05-13 09:46:39 UTC", "User": "root" }, "Author": "Egor Semenchenko [aut, cre, cph] (ORCID:\n),\nVolodymyr Tsybulskyi [ctb] (ORCID:\n),\nIrmtraud M. 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