{ "_id": "6a1ad8e31d7bb097a09e7086", "Package": "crisprDesign", "Title": "Comprehensive design of CRISPR gRNAs for nucleases and base\neditors", "Version": "1.15.0", "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 a comprehensive suite of functions to design and\nannotate CRISPR guide RNA (gRNAs) sequences. This includes on-\nand off-target search, on-target efficiency scoring, off-target\nscoring, full gene and TSS contextual annotations, and SNP\nannotation (human only). It currently support five types of\nCRISPR modalities (modes of perturbations): CRISPR knockout,\nCRISPR activation, CRISPR inhibition, CRISPR base editing, and\nCRISPR knockdown. All types of CRISPR nucleases are supported,\nincluding DNA- and RNA-target nucleases such as Cas9, Cas12a,\nand Cas13d. All types of base editors are also supported. gRNA\ndesign can be performed on reference genomes, transcriptomes,\nand custom DNA and RNA sequences. Both unpaired and paired gRNA\ndesigns are enabled.", "biocViews": "CRISPR, FunctionalGenomics, GeneTarget", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "BugReports": "https://github.com/crisprVerse/crisprDesign/issues", "URL": "https://github.com/crisprVerse/crisprDesign", "LazyData": "true", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev python3 libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:44 UTC", "RemoteUrl": "https://github.com/bioc/crisprDesign", "RemoteRef": "HEAD", "RemoteSha": "2befbcbd01f7de94d304dca44a10eb2414c05c6e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:52:01 UTC", "User": "root" }, "Author": "Jean-Philippe Fortin [aut, cre],\nLuke Hoberecht [aut]", "Maintainer": "Jean-Philippe Fortin ", "MD5sum": "f463f228314a9101e334b878ace9e7b3", "_user": "bioc", "_type": "src", "_file": "crisprDesign_1.15.0.tar.gz", "_fileid": "21841aacc7365d508135c34861c256902efc683787585aa85e8d034e58b5eb64", "_filesize": 2806756, "_sha256": "21841aacc7365d508135c34861c256902efc683787585aa85e8d034e58b5eb64", "_created": "2026-05-30T08:52:01.000Z", "_published": "2026-05-30T12:32:35.607Z", "_jobs": [ { "job": 78637871184, "time": 321, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307004817" }, { "job": 78637871203, "time": 702, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307043575" }, { "job": 78637871198, "time": 695, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307042954" }, { "job": 78637871196, "time": 511, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308188896" }, { "job": 78637871193, "time": 380, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308175391" }, { "job": 78637427272, "time": 463, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306970536" }, { "job": 78637871190, "time": 254, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306997286" }, { "job": 78637871224, "time": 651, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7307038454" }, { "job": 78637871223, "time": 661, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307039881" }, { "job": 78637871228, "time": 659, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307039425" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679562762", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/crisprDesign", "_commit": { "id": "2befbcbd01f7de94d304dca44a10eb2414c05c6e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381124 }, "_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": ">= 4.2.0", "role": "Depends" }, { "package": "crisprBase", "version": ">= 1.1.3", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.77.2", "role": "Imports" }, { "package": "BSgenome", "version": ">= 1.77.1", "role": "Imports" }, { "package": "crisprBowtie", "version": ">= 0.99.8", "role": "Imports" }, { "package": "crisprScore", "version": ">= 1.15.2", "role": "Imports" }, { "package": "GenomeInfoDb", "version": ">= 1.45.7", "role": "Imports" }, { "package": "GenomicFeatures", "version": ">= 1.61.4", "role": "Imports" }, { 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"Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "Rbowtie", "role": "Suggests" }, { "package": "Rbwa", "role": "Suggests" }, { "package": "RCurl", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-29", "n": 1 }, { "week": "2025-44", "n": 11 }, { "week": "2025-45", "n": 10 }, { "week": "2025-46", "n": 2 }, { "week": "2025-47", "n": 3 }, { "week": "2025-49", "n": 5 }, { "week": "2026-10", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "crispr", "functionalgenomics", "genetarget", "bioconductor", "bioconductor-package", "crispr-cas9", "crispr-design", "crispr-target", "genomics-analysis", "grna", "grna-sequence", "grna-sequences", "sgrna", "sgrna-design" ], 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"addCompositeScores", "addConservationScores", "addCutSites", "addDistanceToTss", "addEditedAlleles", "addEditingSites", "addExonTable", "addGeneAnnotation", "addIsoformAnnotation", "addNtcs", "addOffTargetScores", "addOnTargetScores", "addOpsBarcodes", "addPamScores", "addPfamDomains", "addReinitiationFlag", "addRepeats", "addRestrictionEnzymes", "addSequenceFeatures", "addSNPAnnotation", "addSpacerAlignments", "addSpacerAlignmentsIterative", "addTssAnnotation", "addTxTable", "alignments", "alignments<-", "bsgenome", "convertToMinMaxGRanges", "convertToProtospacerGRanges", "crisprNuclease", "customSequences", "cutLength", "cutSites", "designCompleteAnnotation", "designOpsLibrary", "editedAlleles", "enzymeAnnotation", "enzymeAnnotation<-", "exonTable", "findSpacerPairs", "findSpacers", "flattenGuideSet", "geneAnnotation", "geneAnnotation<-", "getBarcodeDistanceMatrix", "getConsensusIsoform", "getMrnaSequences", "getPAMSequence", "getPAMSiteFromStartAndEnd", "getPreMrnaSequences", "getSpacerAlignments", "getSpacerSequence", "getTssObjectFromTxObject", "getTxDb", "getTxInfoDataFrame", "GuideSet", "GuideSet2DataFrames", "mcols", "offTargets", "onTargets", "PairedGuideSet", "pamDistance", "pamLength", "pamOrientation", "pams", "pamSide", "pamSites", "preparePfamTable", "protospacers", "prototypeSequence", "queryTss", "queryTxObject", "rankSpacers", "removeRepeats", "removeSpacersWithSecondaryTargets", "seqnames", "snps", "snps<-", "spacerDistance", "spacerLength", "spacers", "targetOrigin", "tssAnnotation", "tssAnnotation<-", "TxDb2GRangesList", "txTable", "updateOpsLibrary", "validateOpsLibrary" ], "_datasets": [ { "name": "grListExample", "title": "Example of a TxDb object converted to a GRangesList", "object": "grListExample", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "grRepeatsExample", "title": "Example of a GRanges object containing repeat elements", "object": "grRepeatsExample", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "guideSetExample", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3", "object": "guideSetExample", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "guideSetExampleFullAnnotation", "title": "Example of a fully-annotated GuideSet object storing gRNA sequences targeting the CDS of IQSEC3", "object": "guideSetExampleFullAnnotation", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "guideSetExampleWithAlignments", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 with off-target alignments.", "object": "guideSetExampleWithAlignments", "class": [ "GuideSet" ], "fields": [], "table": false, "tojson": false }, { "name": "snpObjectExample", "title": "Example of a GRanges object containing SNPs", "object": "snpObjectExample", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "tssObjectExample", "title": "Example of a GRanges object containing TSS coordinates", "object": "tssObjectExample", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "addCompositeScores", "title": "Add on-target composite score to a GuideSet object.", "topics": [ "addCompositeScores", "addCompositeScores,GuideSet-method", "addCompositeScores,NULL-method", "addCompositeScores,PairedGuideSet-method" ] }, { "page": "addConservationScores", "title": "Add on-target composite score to a GuideSet object.", "topics": [ "addConservationScores", "addConservationScores,GuideSet-method", "addConservationScores,NULL-method", "addConservationScores,PairedGuideSet-method" ] }, { "page": "addDistanceToTss", "title": "Add distance to TSS for a specificed TSS id", "topics": [ "addDistanceToTss", "addDistanceToTss,GuideSet-method", "addDistanceToTss,PairedGuideSet-method" ] }, { "page": "addEditedAlleles", "title": "To add edited alleles for a CRISPR base editing GuideSet", "topics": [ "addEditedAlleles" ] }, { "page": "addEditingSites", "title": "Add optimal editing site for base editing gRNAs.", "topics": [ "addEditingSites", "addEditingSites,GuideSet-method", "addEditingSites,NULL-method", "addEditingSites,PairedGuideSet-method" ] }, { "page": "addExonTable", "title": "Add a gene-specific exon table to a GuideSet object.", "topics": [ "addExonTable" ] }, { "page": "addGeneAnnotation", "title": "Add gene context annotation to a GuideSet object", "topics": [ "addGeneAnnotation", "addGeneAnnotation,GuideSet-method", "addGeneAnnotation,PairedGuideSet-method" ] }, { "page": "addIsoformAnnotation", "title": "Add isoform-specific annotation to a GuideSet object", "topics": [ "addDistanceToTss,NULL-method", "addIsoformAnnotation", "addIsoformAnnotation,GuideSet-method", "addIsoformAnnotation,NULL-method", "addIsoformAnnotation,PairedGuideSet-method" ] }, { "page": "addNtcs", "title": "Add non-targeting control (NTC) sequences to GuideSet", "topics": [ "addNtcs", "addNtcs,GuideSet-method", "addNtcs,NULL-method", "addNtcs,PairedGuideSet-method" ] }, { "page": "addOffTargetScores", "title": "Add CFD and MIT scores to a GuideSet object.", "topics": [ "addOffTargetScores", "addOffTargetScores,GuideSet-method", "addOffTargetScores,NULL-method", "addOffTargetScores,PairedGuideSet-method" ] }, { "page": "addOnTargetScores", "title": "Add on-target scores to a GuideSet object.", "topics": [ "addOnTargetScores", "addOnTargetScores,GuideSet-method", "addOnTargetScores,NULL-method", "addOnTargetScores,PairedGuideSet-method" ] }, { "page": "addOpsBarcodes", "title": "Add optical pooled screening (OPS) barcodes", "topics": [ "addOpsBarcodes" ] }, { "page": "addPamScores", "title": "Add PAM scores to a GuideSet object.", "topics": [ "addPamScores", "addPamScores,GuideSet-method", "addPamScores,NULL-method", "addPamScores,PairedGuideSet-method" ] }, { "page": "addPfamDomains", "title": "Add Pfam domains annotation to GuideSet object", "topics": [ "addPfamDomains", "addPfamDomains,GuideSet-method", "addPfamDomains,NULL-method", "addPfamDomains,PairedGuideSet-method" ] }, { "page": "addReinitiationFlag", "title": "Add a logical flag for gRNAs leading to potential reinitiation", "topics": [ "addReinitiationFlag" ] }, { "page": "addRepeats", "title": "Annotate a GuideSet object with repeat elements", "topics": [ "addRepeats", "addRepeats,GuideSet-method", "addRepeats,NULL-method", "addRepeats,PairedGuideSet-method" ] }, { "page": "addRestrictionEnzymes", "title": "Restriction enzyme recognition sites in spacer sequences", "topics": [ "addRestrictionEnzymes", "addRestrictionEnzymes,GuideSet-method", "addRestrictionEnzymes,NULL-method", "addRestrictionEnzymes,PairedGuideSet-method" ] }, { "page": "addSequenceFeatures", "title": "Add spacer sequence feature annotation columns to a GuideSet object", "topics": [ "addSequenceFeatures", "addSequenceFeatures,GuideSet-method", "addSequenceFeatures,NULL-method", "addSequenceFeatures,PairedGuideSet-method" ] }, { "page": "addSNPAnnotation", "title": "Add SNP annotation to a GuideSet object", "topics": [ "addGeneAnnotation,NULL-method", "addSNPAnnotation", "addSNPAnnotation,GuideSet-method", "addSNPAnnotation,NULL-method", "addSNPAnnotation,PairedGuideSet-method" ] }, { "page": "addSpacerAlignments", "title": "Functions for finding and characterizing on- and off-targets of spacer sequences.", "topics": [ "addSpacerAlignments", "addSpacerAlignments,GuideSet-method", "addSpacerAlignments,NULL-method", "addSpacerAlignments,PairedGuideSet-method", "addSpacerAlignmentsIterative", "addSpacerAlignmentsIterative,GuideSet-method", "addSpacerAlignmentsIterative,NULL-method", "addSpacerAlignmentsIterative,PairedGuideSet-method", "getSpacerAlignments" ] }, { "page": "addTssAnnotation", "title": "Add TSS context annotation to a GuideSet object", "topics": [ "addTssAnnotation", "addTssAnnotation,GuideSet-method", "addTssAnnotation,NULL-method", "addTssAnnotation,PairedGuideSet-method" ] }, { "page": "addTxTable", "title": "Add a gene-specific transcript table to a GuideSet object.", "topics": [ "addTxTable" ] }, { "page": "completeSpacers", "title": "Get complete spacer information", "topics": [ "completeSpacers", "getPAMSequence", "getPAMSiteFromStartAndEnd", "getSpacerSequence" ] }, { "page": "convertToMinMaxGRanges", "title": "Convert a GuideSet object into a GRanges containing the range of all targeting gRNAs.", "topics": [ "convertToMinMaxGRanges" ] }, { "page": "convertToProtospacerGRanges", "title": "Convert PAM site coordinates to protospacer start and end coordinates", "topics": [ "convertToProtospacerGRanges" ] }, { "page": "GuideSet-class", "title": "An S4 class to store CRISPR gRNA sequences with modular annotations.", "topics": [ "addCutSites", "addCutSites,GuideSet-method", "alignments", "alignments,GuideSet-method", "alignments<-", "alignments<-,GuideSet-method", "bsgenome", "bsgenome,GuideSet-method", "crisprNuclease", "crisprNuclease,GuideSet-method", "customSequences", "customSequences,GuideSet-method", "cutSites,GuideSet-method", "editedAlleles", "editedAlleles,GuideSet-method", "enzymeAnnotation", "enzymeAnnotation,GuideSet-method", "enzymeAnnotation<-", "enzymeAnnotation<-,GuideSet-method", "exonTable", "exonTable,GuideSet-method", "geneAnnotation", "geneAnnotation,GuideSet-method", "geneAnnotation<-", "geneAnnotation<-,GuideSet-method", "GuideSet", "GuideSet-class", "offTargets", "offTargets,GuideSet-method", "onTargets", "onTargets,GuideSet-method", "pamLength,GuideSet-method", "pams,GuideSet-method", "pamSide,GuideSet-method", "pamSites", "pamSites,GuideSet-method", "protospacers", "protospacers,GuideSet-method", "prototypeSequence,GuideSet-method", "snps", "snps,GuideSet-method", "snps<-", "snps<-,GuideSet-method", "spacerLength,GuideSet-method", "spacers", "spacers,GuideSet-method", "targetOrigin", "targetOrigin,GuideSet-method", "tssAnnotation", "tssAnnotation,GuideSet-method", "tssAnnotation<-", "tssAnnotation<-,GuideSet-method", "txTable", "txTable,GuideSet-method" ] }, { "page": "designCompleteAnnotation", "title": "One-step gRNA design and annotation function", "topics": [ "designCompleteAnnotation" ] }, { "page": "designOpsLibrary", "title": "Design gRNA library for optical pooled screening", "topics": [ "designOpsLibrary" ] }, { "page": "findSpacerPairs", "title": "Find pairs of CRISPR gRNA spacers from a pair of genomic regions.", "topics": [ "findSpacerPairs" ] }, { "page": "findSpacers", "title": "Find CRISPR gRNA spacer sequences from a set of DNA sequences.", "topics": [ "findSpacers" ] }, { "page": "flattenGuideSet", "title": "Create a list of annotation tables from a GuideSet object", "topics": [ "flattenGuideSet" ] }, { "page": "getBarcodeDistanceMatrix", "title": "Get distance between query and target sets of barcodes", "topics": [ "getBarcodeDistanceMatrix" ] }, { "page": "getConsensusIsoform", "title": "Get the genomic ranges of a consensus isoform", "topics": [ "getConsensusIsoform" ] }, { "page": "getMrnaSequences", "title": "Retrieve mRNA sequences", "topics": [ "getMrnaSequences" ] }, { "page": "getPreMrnaSequences", "title": "Retrieve pre-mRNA sequences", "topics": [ "getPreMrnaSequences" ] }, { "page": "getTssObjectFromTxObject", "title": "Extract TSS coordinates from a gene model object", "topics": [ "getTssObjectFromTxObject" ] }, { "page": "getTxDb", "title": "getTxDb", "topics": [ "getTxDb" ] }, { "page": "getTxInfoDataFrame", "title": "To obtain a DataFrame of transcript-specific CDS and mRNA coordinates", "topics": [ "getTxInfoDataFrame" ] }, { "page": "grListExample", "title": "Example of a TxDb object converted to a GRangesList", "topics": [ "grListExample" ] }, { "page": "grRepeatsExample", "title": "Example of a GRanges object containing repeat elements", "topics": [ "grRepeatsExample" ] }, { "page": "GuideSet2DataFrames", "title": "Create a list of annotation tables from a GuideSet object", "topics": [ "GuideSet2DataFrames" ] }, { "page": "guideSetExample", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3", "topics": [ "guideSetExample" ] }, { "page": "guideSetExampleFullAnnotation", "title": "Example of a fully-annotated GuideSet object storing gRNA sequences targeting the CDS of IQSEC3", "topics": [ "guideSetExampleFullAnnotation" ] }, { "page": "guideSetExampleWithAlignments", "title": "Example of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 with off-target alignments.", "topics": [ "guideSetExampleWithAlignments" ] }, { "page": "PairedGuideSet-class", "title": "An S4 class to store pairs of CRISPR gRNA sequences.", "topics": [ "crisprNuclease,PairedGuideSet-method", "cutLength", "cutLength,PairedGuideSet-method", "cutSites,PairedGuideSet-method", "PairedGuideSet", "PairedGuideSet-class", "pamDistance", "pamDistance,PairedGuideSet-method", "pamLength,PairedGuideSet-method", "pamOrientation", "pamOrientation,PairedGuideSet-method", "pams,PairedGuideSet-method", "pamSide,PairedGuideSet-method", "pamSites,PairedGuideSet-method", "protospacers,PairedGuideSet-method", "spacerDistance", "spacerDistance,PairedGuideSet-method", "spacerLength,PairedGuideSet-method", "spacers,PairedGuideSet-method" ] }, { "page": "preparePfamTable", "title": "Obtain Pfam domains from biomaRt", "topics": [ "preparePfamTable" ] }, { "page": "queryTss", "title": "Convenience function to search for TSS coordinates.", "topics": [ "queryTss" ] }, { "page": "queryTxObject", "title": "Convenience function to search for gene coordinates.", "topics": [ "queryTxObject" ] }, { "page": "rankSpacers", "title": "Recommended gRNA ranking", "topics": [ "rankSpacers" ] }, { "page": "removeRepeats", "title": "Remove GuideSet gRNAs that overlap repeat elements", "topics": [ "removeRepeats", "removeRepeats,GuideSet-method", "removeRepeats,NULL-method", 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