REpatternFile_default   REpatternFile_default
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
filterOffTarget         filter off-targets and generate reports.
filtergRNAs             Filter gRNAs
findgRNAs               Find potential gRNAs
gRNA.backbone_default   gRNA.backbone_default
getOfftargetScore       Calculate score for each off target
getOfftargetWithBulge   Identify off-targets with bulges for
                        target-specific gRNAs designed for CRISPR-Cas9
                        systems.
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
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""
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
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
