{ "_id": "6a1adad71d7bb097a09e8c1e", "Package": "crisprShiny", "Title": "Exploring curated CRISPR gRNAs via Shiny", "Version": "1.9.0", "Date": "2026-02-23", "Authors@R": "c(\nperson(\"Jean-Philippe\", \"Fortin\", email = \"fortin946@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Luke\", \"Hoberecht\", email = \"lukehob3@gmail.com\", role = c(\"aut\"))\n)", "Description": "Provides means to interactively visualize guide RNAs\n(gRNAs) in GuideSet objects via Shiny application. This GUI can\nbe self-contained or as a module within a larger Shiny app. The\ncontent of the app reflects the annotations present in the\npassed GuideSet object, and includes intuitive tools to\nexamine, filter, and export gRNAs, thereby making gRNA design\nmore user-friendly.", "biocViews": "CRISPR, FunctionalGenomics, GeneTarget, GUI", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "BugReports": "https://github.com/crisprVerse/crisprShiny/issues", "URL": "https://github.com/crisprVerse/crisprShiny", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\npython3 libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:24 UTC", "RemoteUrl": "https://github.com/bioc/crisprShiny", "RemoteRef": "HEAD", "RemoteSha": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:52:56 UTC", "User": "root" }, "Author": "Jean-Philippe Fortin [aut, cre],\nLuke Hoberecht [aut]", "Maintainer": "Jean-Philippe Fortin ", "MD5sum": "7d21518de1a89108d56978a06c5f68f6", "_user": "bioc", "_type": "src", "_file": "crisprShiny_1.9.0.tar.gz", "_fileid": "a3171fd331b8688bddeac029a03375005c5ab44dc0d038b17d0e18fe4f42bd5e", "_filesize": 2177962, "_sha256": "a3171fd331b8688bddeac029a03375005c5ab44dc0d038b17d0e18fe4f42bd5e", "_created": "2026-05-30T08:52:56.000Z", "_published": "2026-05-30T12:40:55.388Z", "_jobs": [ { "job": 78637917160, "time": 311, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307009656" }, { "job": 78637917162, "time": 618, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307040707" }, { "job": 78637917169, "time": 644, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307043138" }, { "job": 78637917156, "time": 323, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308209867" }, { "job": 78637917159, "time": 631, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308242631" }, { "job": 78637512846, "time": 429, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306976363" }, { "job": 78637917147, "time": 266, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307004617" }, { "job": 78637917197, "time": 700, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307048725" }, { "job": 78637917195, "time": 555, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307034463" }, { "job": 78637917181, "time": 556, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307035030" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/crisprShiny", "_commit": { "id": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381344 }, "_maintainer": { "name": "Jean-Philippe Fortin", "email": "fortin946@gmail.com", "login": "jfortin1", "bluesky": "@jp-fortin.bsky.social", "linkedin": "in/jean-philippe-fortin-98a68a47", "description": "Freelancer | Father of the @crisprVerse ", "uuid": 2328424 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "shiny", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "crisprBase", "role": "Imports" }, { "package": "crisprDesign", "role": "Imports" }, { "package": "crisprScore", "role": "Imports" }, { "package": "crisprViz", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "htmlwidgets", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pwalign", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "shinyBS", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "waiter", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shinyFeedback", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-47", "n": 3 }, { "week": "2026-09", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "crispr", "functionalgenomics", "genetarget", "gui", "crispr-analysis", "crispr-design", "shiny" ], "_stars": 2, "_contributors": [ { "user": "jwokaty", "count": 8, "uuid": 1744257 }, { "user": "jfortin1", "count": 4, "uuid": 2328424 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 243, "source": "https://www.bioconductor.org/packages/stats/bioc/crisprShiny" }, "_devurl": "https://github.com/crisprverse/crisprshiny", "_searchresults": 11, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/crisprShiny.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/crisprverse/crisprshiny", "_realowner": "bioc", "_cranurl": false, "_exports": [ "crisprServer", "crisprShiny", "crisprUI" ], "_datasets": [ { "name": "guideSetExample_basic", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS", "object": "guideSetExample_basic", "file": "guideSetExample_basic.rda", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "guideSetExample_kras", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS", "object": "guideSetExample_kras", "file": "guideSetExample_kras.rda", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "guideSetExample_kras_be", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS", "object": "guideSetExample_kras_be", "file": "guideSetExample_kras_be.rda", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "guideSetExample_ntcs", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS and NTCs", "object": "guideSetExample_ntcs", "file": "guideSetExample_ntcs.rda", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "tooltipAnnotation", "title": "List of tooltip annotations", "object": "tooltipAnnotation", "file": "tooltipAnnotation.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "tss_kras", "title": "Example of a 'GenomicRanges' object storing annotated TSS ranges for the human gene KRAS", "object": "tss_kras", "file": "tss_kras.rda", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "txdb_kras", "title": "Example of a 'CompressedGenomicRangesList' object storing annotated ranges for the human gene KRAS", "object": "txdb_kras", "file": "txdb_kras.rda", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "crisprServer", "title": "Server component for crisprShiny App", "topics": [ "crisprServer" ] }, { "page": "crisprShiny", "title": "Interactive visualization of GuideSets via Shiny applications", "topics": [ "crisprShiny" ] }, { "page": "crisprUI", "title": "UI component for crisprShiny App", "topics": [ "crisprUI" ] }, { "page": "guideSetExample_basic", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS", "topics": [ "guideSetExample_basic" ] }, { "page": "guideSetExample_kras", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS", "topics": [ "guideSetExample_kras" ] }, { "page": "guideSetExample_kras_be", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS", "topics": [ "guideSetExample_kras_be" ] }, { "page": "guideSetExample_ntcs", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS and NTCs", "topics": [ "guideSetExample_ntcs" ] }, { "page": "tooltipAnnotation", "title": "List of tooltip annotations", "topics": [ "tooltipAnnotation" ] }, { "page": "tss_kras", "title": "Example of a 'GenomicRanges' object storing annotated TSS ranges for the human gene KRAS", "topics": [ "tss_kras" ] }, { "page": "txdb_kras", "title": "Example of a 'CompressedGenomicRangesList' object storing annotated ranges for the human gene KRAS", "topics": [ "txdb_kras" ] } ], "_readme": "https://github.com/bioc/crisprShiny/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "BiocVersion", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "checkmate", "cigarillo", "cli", "clipr", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "crayon", "crisprBase", "crisprBowtie", "crisprDesign", "crisprScore", "crisprScoreData", "crisprViz", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dplyr", "DT", "ensembldb", "evaluate", "ExperimentHub", "farver", "fastmap", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "Gviz", "here", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "interp", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "later", "lattice", "latticeExtra", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "nnet", "openssl", "otel", "pillar", "pkgconfig", "png", "prettyunits", "progress", "promises", "ProtGenerics", "purrr", "pwalign", "R6", "randomForest", "rappdirs", "Rbowtie", "RColorBrewer", "Rcpp", "RcppEigen", "RcppTOML", "RCurl", "readr", "restfulr", "reticulate", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "rprojroot", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "shiny", "shinyBS", "shinyjs", "snow", "sourcetools", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "txdbmaker", "tzdb", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "vroom", "waiter", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "intro.Rmd", "filename": "intro.html", "title": "Introduction to crisprShiny", "author": "Luke Hoberecht, Jean-Philippe Fortin", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Creating self-contained Shiny applications", "Basic GuideSet (no additional annotations)", "Fully-annotated GuideSet", "On-targets table", "gRNA filters", "Nucleotide content", "Off-target count", "Scores", "Genomic Features", "Isoform-specific parameters", "Promoter targeting parameters", "Visualizing on-targets", "gRNA-specific anntations/list columns", "On- and Off-targets", "Gene Annotation", "TSS Annotation", "Restriction Enzyme", "SNPs", "Customized apps using Shiny modules", "Session Info" ], "created": "2023-07-26 22:45:54", "modified": "2023-10-19 18:05:17", "commits": 2 } ], "_score": 4.819543935541869, "_indexed": true, "_nocasepkg": "crisprshiny", "_universes": [ "bioc", "jfortin1", "crisprverse" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-05-30T08:58:33.000Z", "distro": "noble", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "83e7ea85572349e4288574d79a59d4a0da53482529ed72bd91acbee1caa9a4d7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.6.0", "os": "linux", "version": "1.9.0", "date": "2026-05-30T08:59:08.000Z", "distro": "noble", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "900aba7bbd5915402166d79c50c86379bccf29218eb3c364490056b0f920b0bd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-05-30T12:32:14.000Z", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "776834495a34839bd6d7f59f84dfb42e0439e813db067dce877534ec9d0936aa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.6.0", "os": "mac", "version": "1.9.0", "date": "2026-05-30T12:33:50.000Z", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "15321cdf7038181c44cd33897c65d999e879d3409aba13e729671c0f10f203e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-05-30T08:58:17.000Z", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "eba9294a9f6ec2c164b2b8ade77afa7718771f51dd2ee0b8cd4475afd0791127", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-05-30T08:58:51.000Z", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "d99ef04c87bbe7a5049ffa19d79ecb32c93edbaf15897f49cb56ebe984506585", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-05-30T08:57:06.000Z", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "efbccb6feb363c7377929f3af8a5143a6030058c921a231634efd62a0a988fe2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" }, { "r": "4.6.0", "os": "win", "version": "1.9.0", "date": "2026-05-30T08:57:18.000Z", "commit": "21f982dd4c261fc0c8f4c20c13cccfd5fa2a86c4", "fileid": "6097b32f9d0f8e0e930fe7b46614464368a688caacb58176bba234deb74c8b3c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679590939" } ] }