Design of guide RNAs in CRISPR genome-editing systems

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Documentation for package ‘CRISPRseek’ version 1.49.0

• 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