{ "_id": "6aca7bdefe5cc25786e8a022", "Package": "crisprBowtie", "Version": "1.17.0", "Date": "2025-07-22", "Title": "Bowtie-based alignment of CRISPR gRNA spacer sequences", "Authors@R": "c(\nperson(\"Jean-Philippe\", \"Fortin\", email = \"fortin946@gmail.com\", role = c(\"aut\", \"cre\")))", "biocViews": "CRISPR, FunctionalGenomics, Alignment", "Description": "Provides a user-friendly interface to map on-targets and\noff-targets of CRISPR gRNA spacer sequences using bowtie. The\nalignment is fast, and can be performed using either\ncommonly-used or custom CRISPR nucleases. The alignment can\nwork with any reference or custom genomes. Both DNA- and\nRNA-targeting nucleases are supported.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.2.1", "VignetteBuilder": "knitr", "BugReports": "https://github.com/crisprVerse/crisprBowtie/issues", "URL": "https://github.com/crisprVerse/crisprBowtie", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:50 UTC", "RemoteUrl": "https://github.com/bioc/crisprBowtie", "RemoteRef": "HEAD", "RemoteSha": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 16:24:56 UTC", "User": "root" }, "Author": "Jean-Philippe Fortin [aut, cre]", "Maintainer": "Jean-Philippe Fortin ", "_user": "bioc", "_type": "src", "_file": "crisprBowtie_1.17.0.tar.gz", "_fileid": "https://r2.ropensci.org/527febc587199c8814b0a8f86762356b9469d4339d268a8f3dd73ae02a546670", "_filesize": 126717, "_sha256": "527febc587199c8814b0a8f86762356b9469d4339d268a8f3dd73ae02a546670", "_expires": "2027-01-18T17:54:36.000Z", "_created": "2026-10-10T16:24:56.000Z", "_published": "2026-10-10T17:54:37.947Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 6 }, "_upstream": "https://github.com/bioc/crisprBowtie", "_commit": { "id": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381070 }, "_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": "resolute", "_jobs": [ { "job": 114258326056, "time": 188, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11676315691" }, { "job": 114258326069, "time": 389, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11675576879" }, { "job": 114258326059, "time": 357, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11675486963" }, { "job": 114258326104, "time": 239, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11678021097" }, { "job": 114258326105, "time": 303, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11677327483" }, { "job": 114257215676, "time": 332, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11675865773" }, { "job": 114258326138, "time": 166, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11675721221" }, { "job": 114258326187, "time": 278, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11675856402" }, { "job": 114258326101, "time": 278, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11675975624" }, { "job": 114258326297, "time": 254, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11676450093" } ], "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "crisprBase", "version": ">= 0.99.15", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Rbowtie", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "crispr", "functionalgenomics", "alignment", "aligner", "bioconductor", "bioconductor-package", "bowtie", "crispr-analysis", "crispr-cas9", "crispr-design", "crispr-target", "grna", "grna-sequence", "grna-sequences", "sgrna", "sgrna-design" ], "_stars": 3, "_contributors": [ { "user": "jfortin1", "count": 14, "uuid": 2328424 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 490, "source": "https://www.bioconductor.org/packages/stats/bioc/crisprBowtie" }, "_devurl": "https://github.com/crisprverse/crisprbowtie", "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/crisprBowtie.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/crisprverse/crisprbowtie", "_realowner": "bioc", "_cranurl": false, "_exports": [ "runBowtie", "runCrisprBowtie" ], "_help": [ { "page": "runBowtie", "title": "Perform short sequence alignment with bowtie", "topics": [ "runBowtie" ] }, { "page": "runCrisprBowtie", "title": "Perform CRISPR gRNA spacer alignment with bowtie", "topics": [ "runCrisprBowtie" ] } ], "_readme": "https://github.com/bioc/crisprBowtie/raw/HEAD/README.md", "_rundeps": [ "askpass", "BH", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "BSgenome", "cigarillo", "cli", "clipr", "codetools", "cpp11", "crayon", "crisprBase", "curl", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "glue", "hms", "httr", "IRanges", "jsonlite", "lambda.r", "lifecycle", "magrittr", "matrixStats", "mime", "openssl", "pillar", "pkgconfig", "prettyunits", "progress", "R6", "Rbowtie", "RCurl", "readr", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Vectors", "Seqinfo", "snow", "stringi", "stringr", "sys", "tibble", "tidyselect", "tzdb", "utf8", "vctrs", "vroom", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "crisprBowtie.Rmd", "filename": "crisprBowtie.html", "title": "crisprBowtie: alignment of gRNA spacer sequences using bowtie", "author": "Jean-Philippe Fortin", "engine": "knitr::rmarkdown", "headings": [ "Overview of crisprBowtie", "Installation and getting started", "Software requirements", "OS Requirements", "Installation from Bioconductor", "Building a bowtie index", "Alignment using runCrisprBowtie", "Applications beyond CRISPR", "Example using RNAi (siRNA design)", "Reproducibility", "References" ], "created": "2021-09-21 18:58:48", "modified": "2022-10-17 18:41:26", "commits": 9 } ], "_score": 5.857332496431268, "_indexed": true, "_nocasepkg": "crisprbowtie", "_universes": [ "bioc", "jfortin1", "crisprverse" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.0", "date": "2026-10-10T16:29:37.000Z", "distro": "resolute", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/eaae4ff506ae07e49c4799ca18bff493786f6262969411ce1902bbf1fbefa80e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.6.1", "os": "linux", "version": "1.17.0", "date": "2026-10-10T16:29:08.000Z", "distro": "resolute", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/0c33cf941ccb300d2d3cf1d32873786532b2a54a0413b7ddf1af47fef6daac62", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.5.3", "os": "mac", "version": "1.17.0", "date": "2026-10-10T17:52:17.000Z", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/f2154406e6200d85503c832ec0394a8f36edf6783005865861f0d153992e377b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.6.1", "os": "mac", "version": "1.17.0", "date": "2026-10-10T17:51:19.000Z", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/a9165288a576ec29c0f4630dc4f44ddadebf2cb8db4461b543fa27f4c692bc4f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.0", "date": "2026-10-10T16:28:10.000Z", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/4c60a51ca66cbcd48817ec38e117fb7c6ed184cb5bc7cb4d9f85abcc79347799", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.7.0", "os": "win", "version": "1.17.0", "date": "2026-10-10T16:27:40.000Z", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/ada9af392821a34f9eb22df0f14f96893f21ce745f55e1a43ce9142c0f518d89", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.5.3", "os": "win", "version": "1.17.0", "date": "2026-10-10T16:27:54.000Z", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/c77fc842eed6e2a17fee01f560dad0fc281e68d793ab505252c96be312a2e2fa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" }, { "r": "4.6.1", "os": "win", "version": "1.17.0", "date": "2026-10-10T16:27:40.000Z", "commit": "37de0a3c6e7a9e2ca46434ca860d8457f4d1c4e3", "fileid": "https://r2.ropensci.org/176cff49677824dc1e779ffb70e1eaffcfd29771c7e06600184364401c9b37ce", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38067198273" } ] }