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

Documentation for package ‘CRISPRseek’ version 1.20.0

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
filtergRNAs	Filter gRNAs
filterOffTarget	filter off targets and generate reports.
findgRNAs	Find potential gRNAs
foldgRNAs	Fold gRNAs with the gRNA backbone constant region
getOfftargetScore	Calculate score for each off target
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
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