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


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Documentation for package ‘CRISPRseek’ version 1.45.0

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CRISPRseek-package Design of target-specific guide RNAs (gRNAs) in CRISPR-Cas9, genome-editing systems
annotateOffTargets annotate off targets
buildFeatureVectorForScoring Build feature vectors
calculategRNAEfficiency Calculate gRNA Efficiency
compare2Sequences Compare 2 input sequences/sequence sets for possible guide RNAs (gRNAs)
CRISPRseek Design of target-specific guide RNAs (gRNAs) in CRISPR-Cas9, genome-editing systems
deepCpf1 DeepCpf1 Algorithm for predicting CRISPR-Cpf1 gRNA Efficacy
filtergRNAs Filter gRNAs
filterOffTarget filter off targets and generate reports.
findgRNAs Find potential gRNAs
getOfftargetScore Calculate score for each off target
isPatternUnique Output whether the input patterns occurs only once in the sequence
offTargetAnalysis Design target-specific guide RNAs for CRISPR-Cas9 system in one function
offTargetAnalysisWithoutBSgenome Design of target-specific guide RNAs for CRISPR-Cas9 system in one function without BSgenome
predictRelativeFreqIndels Predict insertions and deletions induced by CRISPR/Cas9 editing
searchHits Search for off targets in a sequence as DNAString
searchHits2 Search for off targets
translatePattern translate pattern from IUPAC Extended Genetic Alphabet to regular expression
uniqueREs Output restriction enzymes that recognize only the gRNA cleavage sites
writeHits Write the hits of sequence search from a sequence to a file
writeHits2 Write the hits of sequence search to a file