# Generated by roxygen2: do not edit by hand

export(REpatternFile_default)
export(annotateOffTargets)
export(buildFeatureVectorForScoring)
export(calculategRNAEfficiency)
export(chromToExclude_default)
export(compare2Sequences)
export(deepCpf1)
export(featureWeightMatrixFile_default)
export(filterOffTarget)
export(filtergRNAs)
export(findgRNAs)
export(gRNA.backbone_default)
export(getOfftargetScore)
export(getOfftargetWithBulge)
export(isPatternUnique)
export(mismatch.activity.file_default)
export(mismatch.activity.file_default_xlsx)
export(offTargetAnalysis)
export(predictRelativeFreqIndels)
export(searchHits)
export(searchHits2)
export(subPAM.activity_default)
export(translatePattern)
export(uniqueREs)
export(weights_default)
export(writeHits)
export(writeHits2)
import(keras)
import(utils)
importFrom(BSgenome,getSeq)
importFrom(BSgenome,seqnames)
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,do.call)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,grep)
importFrom(BiocGenerics,lapply)
importFrom(BiocGenerics,order)
importFrom(BiocGenerics,rbind)
importFrom(BiocGenerics,relist)
importFrom(BiocGenerics,rep.int)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,subset)
importFrom(BiocGenerics,table)
importFrom(BiocGenerics,toTable)
importFrom(BiocGenerics,unlist)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PDict)
importFrom(Biostrings,RNAStringSet)
importFrom(Biostrings,alphabetFrequency)
importFrom(Biostrings,complement)
importFrom(Biostrings,extractAt)
importFrom(Biostrings,hasLetterAt)
importFrom(Biostrings,isMatchingAt)
importFrom(Biostrings,matchPDict)
importFrom(Biostrings,matchPattern)
importFrom(Biostrings,nchar)
importFrom(Biostrings,neditAt)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,replaceAt)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,substring)
importFrom(Biostrings,writeXStringSet)
importFrom(DelayedArray,mean)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,intersect)
importFrom(GenomicRanges,setdiff)
importFrom(IRanges,IRanges)
importFrom(IRanges,IRangesList)
importFrom(IRanges,PartitioningByEnd)
importFrom(IRanges,Views)
importFrom(IRanges,findOverlaps)
importFrom(IRanges,overlapsAny)
importFrom(IRanges,reverse)
importFrom(IRanges,width)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,elementNROWS)
importFrom(S4Vectors,merge)
importFrom(S4Vectors,orderIntegerPairs)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,unstrsplit)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(Seqinfo,seqnames)
importFrom(XVector,subseq)
importFrom(data.table,as.data.table)
importFrom(dplyr,ends_with)
importFrom(dplyr,mutate_if)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(gtools,permutations)
importFrom(hash,hash)
importFrom(hash,values)
importFrom(methods,as)
importFrom(mltools,one_hot)
importFrom(openxlsx,read.xlsx)
importFrom(openxlsx,write.xlsx)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parLapply)
importFrom(reticulate,conda_create)
importFrom(reticulate,conda_install)
importFrom(reticulate,conda_list)
importFrom(reticulate,install_miniconda)
importFrom(reticulate,py_available)
importFrom(reticulate,py_config)
importFrom(reticulate,py_discover_config)
importFrom(reticulate,py_install)
importFrom(reticulate,py_module_available)
importFrom(reticulate,py_run_string)
importFrom(reticulate,source_python)
importFrom(reticulate,use_condaenv)
importFrom(rhdf5,H5Fopen)
importFrom(rhdf5,h5closeAll)
importFrom(rhdf5,h5createFile)
importFrom(rhdf5,h5write)
importFrom(rio,import)
importFrom(rlang,abort)
importFrom(rlang,arg_match)
importFrom(rlang,call_match)
importFrom(rlang,inform)
importFrom(rlang,warn)
importFrom(seqinr,s2c)
importFrom(stats,predict)
importFrom(stringr,str_c)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_sub)
importFrom(stringr,str_to_lower)
importFrom(stringr,str_to_upper)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.table)
