DOI: 10.18129/B9.bioc.CRISPRseek    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CRISPRseek.

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

Bioconductor version: 3.8

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. This package leverages Biostrings and BSgenome packages.

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

Maintainer: Lihua Julie Zhu <julie.zhu at>

Citation (from within R, enter citation("CRISPRseek")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script CRISPRseek Vignette
PDF   Reference Manual
Text   NEWS


biocViews CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software
Version 1.22.1
In Bioconductor since BioC 2.14 (R-3.1) (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
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CRISPRseek_1.22.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) CRISPRseek_1.22.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: