{ "_id": "6a102ff8acfb0bcc41c9528f", "Package": "Ularcirc", "Type": "Package", "Title": "Shiny app for canonical and back splicing analysis (i.e.\ncircular and mRNA analysis)", "Version": "1.31.0", "Authors@R": "person (\"David\", \"Humphreys\", email=\"d.humphreys@victorchang.edu.au\", \nrole = c(\"aut\",\"cre\"))", "Description": "Ularcirc reads in STAR aligned splice junction files and\nprovides visualisation and analysis tools for splicing\nanalysis. Users can assess backsplice junctions and forward\ncanonical junctions.", "biocViews": "DataRepresentation,Visualization, Genetics, Sequencing,\nAnnotation, Coverage, AlternativeSplicing, DifferentialSplicing", "License": "file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-12 06:03:15 UTC", "RemoteUrl": "https://github.com/bioc/Ularcirc", "RemoteRef": "HEAD", "RemoteSha": "9e0304952edda76ebf11fb86d2fa5a76b092a3be", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 11:26:13 UTC", "User": "root" }, "Author": "David Humphreys [aut, cre]", "Maintainer": "David Humphreys ", "MD5sum": "f7b4dac4742dee3af25009059206529b", "_user": "bioc", "_type": "src", "_file": "Ularcirc_1.31.0.tar.gz", "_fileid": 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}, { "week": "2026-20", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "datarepresentation", "visualization", "genetics", "sequencing", "annotation", "coverage", "alternativesplicing", "differentialsplicing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 348, "source": "https://www.bioconductor.org/packages/stats/bioc/Ularcirc" }, "_mentions": 2, "_searchresults": 6, "_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/readme.html", "extra/readme.md", "extra/Ularcirc.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "BSJ_details", 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Can accept two different formats, Ularcirc or generic.", "topics": [ "BSJ_details" ] }, { "page": "bsj_fastq_generate", "title": "bsj_fastq_generate", "topics": [ "bsj_fastq_generate" ] }, { "page": "bsj_to_circRNA_sequence", "title": "bsj_to_circRNA_sequence", "topics": [ "bsj_to_circRNA_sequence" ] }, { "page": "chimericFilters", "title": "chimericFilters", "topics": [ "chimericFilters" ] }, { "page": "chimericStats", "title": "chimericStats", "topics": [ "chimericStats" ] }, { "page": "circSequence", "title": "circSequence This function returns pre-defined full length circRNA sequences.", "topics": [ "circSequence" ] }, { "page": "Compatible_Annotation_DBs", "title": "Compatible_Annotation_DBs", "topics": [ "Compatible_Annotation_DBs" ] }, { "page": "FilterChimeric_Ularcirc", "title": "Wrapper function for Ularcirc shiny app which expects a list of objects to be returned", "topics": [ "FilterChimeric_Ularcirc" ] }, { "page": "FilterChimericJuncs", "title": "FilterChimericJuncs", "topics": [ "FilterChimericJuncs" ] }, { "page": "Junction_Sequence_from_Genome", "title": "Grab_BS_Junc_Sequence", "topics": [ "Junction_Sequence_from_Genome" ] }, { "page": "load_miRBase_fasta", "title": "load_miRBase_fasta This function extracts species specific mirbase sequences as a Biostrings RNAstringset.", "topics": [ "load_miRBase_fasta" ] }, { "page": "loadSTAR_chimeric", "title": "loadSTAR_chimeric", "topics": [ "loadSTAR_chimeric" ] }, { "page": "miR_binding_site_Analysis", "title": "miR_binding_site_Analysis This function analyses a genomic (RNA or DNA) sequence for matching miRNA seed sequences.", "topics": [ "miR_binding_site_Analysis" ] }, { "page": "plot_AllJunctions", "title": "plot_AllJunctions", "topics": [ "plot_AllJunctions" ] }, { "page": "RAD_score", "title": "RAD_score", "topics": [ "RAD_score" ] }, { "page": "SelectUniqueJunctions", "title": "SelectUniqueJunctions", "topics": [ "SelectUniqueJunctions" ] }, { "page": "sequence_from_exon_coords", "title": "sequence_from_exon_coords", "topics": [ "sequence_from_exon_coords" ] }, { "page": "Ularcirc", "title": "Ularcirc", "topics": [ "Ularcirc" ] } ], "_readme": "https://github.com/bioc/Ularcirc/raw/HEAD/readme.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationHub", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocParallel", "BiocVersion", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "cigarillo", "cli", "codetools", "commonmark", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "dir.expiry", "dplyr", "DT", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomeInfoDbData", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggplotify", "ggrepel", "glue", "gridGraphics", "gsubfn", "gtable", "highr", "htmltools", 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"Ularcirc.Rmd", "filename": "Ularcirc.html", "title": "Ularcirc: A shiny application for canonical and back splicing analysis", "author": "David Humphreys, Nicolas Fossat, Patrick Tam, Joshua Ho", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quickstart", "Preparing input data sets", "Splice junction files", "Annotation databases", "Workflow", "Step 1a: Loading annotation data", "Step 1b: Setting filters", "Genomic filters", "circRNA filters", "Step 1c: Loading new data sets", "Step 2a: Saving/loading a project and grouping samples", "Step 2b: Grouping samples", "Step 3a : Generating BSJ counts", "Step 3b : Visualising gene splicing patterns", "Exploring slicing patterns from any genomic region", "Step 5: Sequence analysis of splice/backsplice junctions", "Session Information-----------------------------------" ], "created": "2019-08-23 12:47:47", "modified": "2019-10-24 11:11:32", "commits": 2 } ], "_score": 4.698970004336019, "_indexed": true, "_nocasepkg": "ularcirc", 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