{ "_id": "6a1afd9a1d7bb097a09fe26a", "Package": "SCANVIS", "Type": "Package", "Title": "SCANVIS - a tool for SCoring, ANnotating and VISualizing splice\njunctions", "Version": "1.27.0", "Date": "2019-07-11", "Author": "Phaedra Agius ", "Maintainer": "Phaedra Agius ", "Description": "SCANVIS is a set of annotation-dependent tools for\nanalyzing splice junctions and their read support as\npredetermined by an alignment tool of choice (for example, STAR\naligner). SCANVIS assesses each junction's relative read\nsupport (RRS) by relating to the context of local split reads\naligning to annotated transcripts. SCANVIS also annotates each\nsplice junction by indicating whether the junction is supported\nby annotation or not, and if not, what type of junction it is\n(e.g. exon skipping, alternative 5' or 3' events, Novel Exons).\nUnannotated junctions are also futher annotated by indicating\nwhether it induces a frame shift or not. SCANVIS includes a\nvisualization function to generate static sashimi-style plots\ndepicting relative read support and number of split reads using\narc thickness and arc heights, making it easy for users to spot\nwell-supported junctions. These plots also clearly delineate\nunannotated junctions from annotated ones using designated\ncolor schemes, and users can also highlight splice junctions of\nchoice. Variants and/or a read profile are also incoroporated\ninto the plot if the user supplies variants in bed format\nand/or the BAM file. One further feature of the visualization\nfunction is that users can submit multiple samples of a certain\ndisease or cohort to generate a single plot - this occurs via a\n\"merge\" function wherein junction details over multiple samples\nare merged to generate a single sashimi plot, which is useful\nwhen contrasting cohorots (eg. disease vs control).", "License": "file LICENSE", "VignetteBuilder": "knitr", "biocViews": "Software,ResearchField,Transcriptomics,WorkflowStep,Annotation,Visualization", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:33 UTC", "RemoteUrl": "https://github.com/bioc/SCANVIS", "RemoteRef": "HEAD", "RemoteSha": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:52:09 UTC", "User": "root" }, "MD5sum": "ebb6a211e6ac8d2410382999884b9730", "_user": "bioc", "_type": "src", "_file": "SCANVIS_1.27.0.tar.gz", "_fileid": "003463f7132afa1957326a02f452666d09eff6483ec43bb3ccbcc9c69c7c0365", "_filesize": 618887, "_sha256": "003463f7132afa1957326a02f452666d09eff6483ec43bb3ccbcc9c69c7c0365", "_created": "2026-05-30T09:52:09.000Z", "_published": "2026-05-30T15:09:14.869Z", "_jobs": [ { "job": 78640891493, "time": 220, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307569577" }, { "job": 78640891500, "time": 397, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307587802" }, { "job": 78640891505, "time": 286, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307575694" }, { "job": 78640891497, "time": 225, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7309125650" }, { "job": 78640891511, "time": 196, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7309123192" }, { "job": 78640029794, "time": 254, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307321999" }, { "job": 78640891496, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307561932" }, { "job": 78640891508, "time": 245, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307570547" }, { "job": 78640891503, "time": 244, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307570399" }, { "job": 78640891507, "time": 267, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307572495" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SCANVIS", "_commit": { "id": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380633 }, "_maintainer": { "name": "Phaedra Agius", "email": "pagius@nygenome.org", "login": "agiusp", "description": "Senior Bioinformatics Scientist", "uuid": 8634142 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "IRanges", "role": "Imports" }, { "package": "plotrix", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "software", "researchfield", "transcriptomics", "workflowstep", "annotation", "visualization" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 350, "source": "https://www.bioconductor.org/packages/stats/bioc/SCANVIS" }, "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/SCANVIS.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "gene2roi", "IR2Mat", "ls_url", "SCANVISannotation", "SCANVISlinkvar", "SCANVISmerge", "SCANVISread_STAR", "SCANVISscan", "SCANVISvisual" ], "_datasets": [ { "name": "GBM", "title": "list of 3 TCGA glioblastoma samples, parts thereof, outputs of SCANVISscan and SCANVISlinkvar functions with toy variants supplied for the variant-SJ mapping", "object": "SCANVISexamples", "file": "SCANVISexamples.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "gbm3", "title": "part of a TCGA glioblastoma sample from STAR alignment SJ.tab file", "object": "SCANVISexamples", "file": "SCANVISexamples.RData", "class": [ "matrix", "array" ], "fields": [ "chr", "start", "end", "uniq.reads" ], "rows": 131, "table": true, "tojson": true }, { "name": "gbm3.vcf", "title": "a toy set of 6 variants that pair up with the gbm3 data example", "object": "SCANVISexamples", "file": "SCANVISexamples.RData", "class": [ "matrix", "array" ], "fields": [ "chr", "start", "end", "passedMUT" ], "rows": 8, "table": true, "tojson": true }, { "name": "gen19", "title": "parts of the annotation object created by the SCANVISannotation function when used with the url ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/ which references the gencode v19 GTF file for human hg19", "object": "SCANVISexamples", "file": "SCANVISexamples.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "LUAD", "title": "list of 3 TCGA lung adenocarcinoma samples, parts thereof, outputs of SCANVISscan", "object": "SCANVISexamples", "file": "SCANVISexamples.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "LUSC", "title": "list of 3 TCGA lung squamous cell carcinoma samples, parts thereof, both outputs of SCANVISscan with the second sample being variant-mapped via SCANVISlinkvar", "object": "SCANVISexamples", "file": "SCANVISexamples.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "SCANVIS-package", "title": "SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions", "topics": [ "SCANVIS-package", "SCANVIS" ] }, { "page": "GBM", "title": "list of 3 TCGA glioblastoma samples, parts thereof, outputs of SCANVISscan and SCANVISlinkvar functions with toy variants supplied for the variant-SJ mapping", "topics": [ "GBM" ] }, { "page": "gbm3", "title": "part of a TCGA glioblastoma sample from STAR alignment SJ.tab file", "topics": [ "gbm3" ] }, { "page": "gbm3.vcf", "title": "a toy set of 6 variants that pair up with the gbm3 data example", "topics": [ "gbm3.vcf" ] }, { "page": "gen19", "title": "parts of the annotation object created by the SCANVISannotation function when used with the url ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/ which references the gencode v19 GTF file for human hg19", "topics": [ "gen19" ] }, { "page": "gene2roi", "title": "gene name/s to region of interest", "topics": [ "gene2roi" ] }, { "page": "IR2Mat", "title": "IRanges to Matrix", "topics": [ "IR2Mat" ] }, { "page": "ls_url", "title": "list files available at annotation/gencode url", "topics": [ "ls_url" ] }, { "page": "LUAD", "title": "list of 3 TCGA lung adenocarcinoma samples, parts thereof, outputs of SCANVISscan", "topics": [ "LUAD" ] }, { "page": "LUSC", "title": "list of 3 TCGA lung squamous cell carcinoma samples, parts thereof, both outputs of SCANVISscan with the second sample being variant-mapped via SCANVISlinkvar", "topics": [ "LUSC" ] }, { "page": "SCANVISannotation", "title": "assembles annotation from gtf file into SCANVISreadable format", "topics": [ "SCANVISannotation" ] }, { "page": "SCANVISexamples", "title": "Data for running SCANVISexamples", "topics": [ "SCANVISexamples" ] }, { "page": "SCANVISlinkvar", "title": "maps variants to SCANVISscored junctions", "topics": [ "SCANVISlinkvar" ] }, { "page": "SCANVISmerge", "title": "merges multiple SCANVISsamples", "topics": [ "SCANVISmerge" ] }, { "page": "SCANVISreadSTAR", "title": "upload SJ.tab STAR file in SCANVISuse", "topics": [ "SCANVISread_STAR" ] }, { "page": "SCANVISscan", "title": "SCore and ANnotate splice junctions", "topics": [ "SCANVISscan" ] }, { "page": "SCANVISvisual", "title": "a sashimi-style visualization tool", "topics": [ "SCANVISvisual" ] } ], "_readme": "https://github.com/bioc/SCANVIS/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "cigarillo", "codetools", "cpp11", "crayon", "curl", "DelayedArray", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "httr", "IRanges", "jsonlite", "lambda.r", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "plotrix", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "runningSCANVIS.Rnw", "filename": "runningSCANVIS.pdf", "title": "SCANVIS", "engine": "knitr::knitr", "headings": [], "created": "2019-04-22 20:57:17", "modified": "2019-06-24 17:30:39", "commits": 6 } ], "_score": 4, "_indexed": true, "_nocasepkg": "scanvis", "_universes": [ "bioc", "agiusp" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-05-30T10:38:32.000Z", "distro": "noble", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "1cea690cbc38c93422d24f5a6c7872ae21d80d6327242e57d84ca59cbc684aa4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-05-30T10:37:34.000Z", "distro": "noble", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "489de08e57d5d1993ccfaf0658f12b068a2f038e59185252385cf30b409b14da", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-05-30T15:06:53.000Z", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "11bf8d5f98a43d886cf43b2cd243b0ce6a47b4c6e4944004240afeb8332fa296", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-05-30T15:06:44.000Z", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "33082ccc357f706815a81d1d0211dbb99a8c28d926f4bf75e1aa43d85ec2e83e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-05-30T10:37:04.000Z", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "8d998727f278a35a7d80647d1dbbda16e4eb700cbf561107500934ae346e44d0", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-05-30T10:36:02.000Z", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "5cd0547d88b59410386f03fd999b5c79e4154acca9bcb6a80c02dc44d40fd32e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-05-30T10:35:51.000Z", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "b58d3085feb69ccace00b0ab993812d567bbbfef15968dc73f4dba982d918234", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-05-30T10:36:03.000Z", "commit": "945361b9bbcf86b189aeba2e8f3d6f72e1255bf3", "fileid": "c2728891b7231d966eedfd76f5f3f55a87f9e73758249b279ff2b2d1733dc851", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677233767" } ] }