CRISPRseek v1.12.0

by Lihua Julie Zhu

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

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.

Functions in CRISPRseek

Name Description
calculategRNAEfficiency Calculate gRNA Efficiency
compare2Sequences Compare 2 input sequences/sequence sets for possible guide RNAs (gRNAs)
offTargetAnalysisOfPeakRegions Finding offtargets in given regions
foldgRNAs Fold gRNAs with the gRNA backbone constant region
getOfftargetScore Calculate score for each off target
searchHits Search for off targets
isPatternUnique Output whether the input patterns occurs only once in the sequence
offTargetAnalysis Design of target-specific guide RNAs for CRISPR-Cas9 system in one function
filterOffTarget filter off targets and generate reports.
findgRNAs Find potential gRNAs
annotateOffTargets annotate off targets
buildFeatureVectorForScoring Build feature vectors
uniqueREs Output restriction enzymes that recognize only the gRNA cleavage sites
translatePattern translate pattern from IUPAC Extended Genetic Alphabet to regular expression
CRISPRseek-package Design of target-specific guide RNAs (gRNAs) in CRISPR-Cas9, genome-editing systems
filtergRNAs Filter gRNAs
writeHits Write the hits of sequence search to a file
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