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

## Documentation for package ‘CRISPRseek’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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