DOI: 10.18129/B9.bioc.CRISPRseek  

This package is for version 3.16 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: 3.16

The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor 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. The package also output indels and their frequencies for Cas9 targeted sites.

Author: Lihua Julie Zhu, Paul Scemama, Benjamin R. Holmes, Hervé Pagès, Kai Hu, Hui Mao, 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")):


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biocViews CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software
Version 1.38.0
In Bioconductor since BioC 2.14 (R-3.1) (9 years)
License GPL (>= 2)
Depends R (>= 3.5.0), BiocGenerics, Biostrings
Imports parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, hash, methods, reticulate, rhdf5, XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools
Suggests RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene,, lattice, MASS, tensorflow, testthat
Depends On Me crisprseekplus
Imports Me GUIDEseq, multicrispr
Suggests Me
Links To Me
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