# Design of guide RNAs in CRISPR genome-editing systems

## Documentation for package ‘CRISPRseek’ version 1.48.0

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

## Help Pages

annotateOffTargets | annotate off targets
buildFeatureVectorForScoring | Build feature vectors
calculategRNAEfficiency | Calculate gRNA Efficiency
chromToExclude_default | Default lengthy arguments
compare2Sequences | Compare two input sequences/sequence sets for possible guide RNAs (gRNAs)
deepCpf1 | DeepCpf1 Algorithm for predicting CRISPR-Cpf1 gRNA Efficacy
featureWeightMatrixFile_default | featureWeightMatrixFile_default
filtergRNAs | Filter gRNAs
filterOffTarget | filter off-targets and generate reports.
findgRNAs | Find potential gRNAs
getOfftargetScore | Calculate score for each off target
getOfftargetWithBulge | Identify off-targets with bulges for target-specific gRNAs designed for CRISPR-Cas9 systems.
gRNA.backbone_default | gRNA.backbone_default
isPatternUnique | Output whether the input patterns occurs only once in the sequence
mismatch.activity.file_default | mismatch.activity.file_default
mismatch.activity.file_default_xlsx | mismatch.activity.file_default_xlsx
offTargetAnalysis | Design target-specific guide RNAs for CRISPR-Cas9 system in one function
predictRelativeFreqIndels | Predict insertions and deletions induced by CRISPR/Cas9 editing
predIndelFreq | Function definition place holders that are to be overwritten by reticulate This is to suppress the R CMD check NOTE about "no visible global function""
REpatternFile_default | REpatternFile_default
searchHits | Search for off targets in a sequence as DNAString
searchHits2 | Search for off targets
subPAM.activity_default | subPAM.activity_default
translatePattern | translate pattern from IUPAC Extended Genetic Alphabet to regular expression
uniqueREs | Output restriction enzymes that recognize only the gRNA cleavage sites
weights_default | weights_default
writeHits | Write the hits of sequence search from a sequence to a file
writeHits2 | Write the hits of sequence search to a file