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This is the development version of CRISPRseek; for the stable release version, see CRISPRseek.

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Bioconductor version: Development (3.6)

The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (,, then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.

Author: Lihua Julie Zhu, Benjamin R. Holmes, Herve Pages, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky

Maintainer: Lihua Julie Zhu <julie.zhu at>

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PDF R Script CRISPRseek Vignette
PDF   Reference Manual
Text   NEWS


biocViews CRISPR, GeneRegulation, SequenceMatching, Software
Version 1.17.0
In Bioconductor since BioC 2.14 (R-3.1) (3.5 years)
License GPL (>= 2)
Depends R (>= 3.0.1), BiocGenerics, Biostrings
Imports parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, BiocParallel, hash
Suggests RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Depends On Me crisprseekplus
Imports Me GUIDEseq
Suggests Me
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