{ "_id": "6a19831bacfb0bcc41df9fe7", "Package": "EventPointer", "Type": "Package", "Title": "An effective identification of alternative splicing events using\njunction arrays and RNA-Seq data", "Version": "3.21.0", "Authors@R": "c(person(\"Juan Pablo\",\"Romero\",role=c(\"aut\"),email = \"jpromero@ceit.es\"),\nperson(\"Juan A.\", \"Ferrer-Bonsoms\",role=c(\"aut\",\"cre\"),email = \"jafhernandez@tecnun.es\"),\nperson(\"Pablo\", \"Sacristan\",role=c(\"aut\"),email = \"a904719@alumni.unav.es\"),\nperson(\"Ander\", \"Muniategui\",role=c(\"aut\")),\nperson(\"Fernando\", \"Carazo\",role=c(\"aut\")),\nperson(\"Ander\", \"Aramburu\",role=c(\"aut\")),\nperson(\"Angel\", \"Rubio\",role=c(\"aut\"),email = \"arubio@tecnun.es\")\n)", "Description": "EventPointer is an R package to identify alternative\nsplicing events that involve either simple (case-control\nexperiment) or complex experimental designs such as time course\nexperiments and studies including paired-samples. The algorithm\ncan be used to analyze data from either junction arrays\n(Affymetrix Arrays) or sequencing data (RNA-Seq). In the\nlatter, EventPointer can work with annotated splicing events or\ncan build a splicing graph from the RNA-Seq reads and then\nidentify new and specific alternative splicing events. The\nsoftware returns a data.frame with the detected alternative\nsplicing events: gene name, type of event (cassette,\nalternative 3',...,etc), genomic position, statistical\nsignificance and increment of the percent spliced in (Delta\nPSI) for all the events. The algorithm can generate a series of\nfiles to visualize the detected alternative splicing events in\nIGV. This eases the interpretation of results and the design of\nprimers for standard PCR validation.", "License": "Artistic-2.0", "LazyData": "true", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "biocViews": "AlternativeSplicing, DifferentialSplicing, mRNAMicroarray,\nRNASeq, Transcription, Sequencing, TimeCourse, ImmunoOncology", "VignetteBuilder": "knitr", "Url": "https://github.com/jpromeror/EventPointer", "BugReports": "https://github.com/jpromeror/EventPointer/issues", "Config/pak/sysreqs": "libglpk-dev make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:11 UTC", "RemoteUrl": "https://github.com/bioc/EventPointer", "RemoteRef": "HEAD", "RemoteSha": "afef15f39ef22750f57744b58a9b1e1bad79fba1", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 10:26:57 UTC", "User": "root" }, "Author": "Juan Pablo Romero [aut],\nJuan A. 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Ferrer-Bonsoms, Cesar Lobato & Angel Rubio", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction", "RNA-Seq analysis", "EventPointerBAM", "Events Detection", "step-by-step", "Statistical Analysis", "IGV visualization", "summary", "EventPointerST", "Event Detection", "Get expression and PSI ($\\Psi$)", "Statistical Analysis (Bootstrap Test)", "Statistical Analysis (NO bootstrap)", "Domain Enrichment", "Primers Design", "IGV primers and probes visualization", "Analysis of junction arrays", "Overview of junction arrays", "CDF file creation", "aroma.affymetrix pre-processing pipeline", "EventPointer function", "Multi-Path Events", "junctions arrays (CDF file for Multi-Path)", "Advanced Use", "Events Reclassification", "Statistical Tests", "Alpha parameter for PrepareBam_EP function", "Percent Spliced In", "References", "Session Information" ], "created": "2017-02-17 22:42:51", "modified": "2025-12-16 16:00:34", "commits": 21 } ], "_score": 6.795880017344075, 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