# Generated by roxygen2: do not edit by hand

S3method(annot_snps,GRanges)
S3method(annot_snps,SummarizedExperiment)
export(FilterParam)
export(annot_from_gr)
export(annot_snps)
export(calc_AEI)
export(calc_confidence)
export(calc_edit_frequency)
export(calc_scAEI)
export(correct_strand)
export(filter_clustered_variants)
export(filter_multiallelic)
export(filter_splice_variants)
export(find_de_sites)
export(find_mispriming_sites)
export(find_scde_sites)
export(get_overlapping_snps)
export(get_scAEI_sites)
export(get_splice_sites)
export(make_de_object)
export(mock_rse)
export(pileup_cells)
export(pileup_sites)
export(raer_example)
export(read_sparray)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(SummarizedExperiment)
importFrom(BSgenome,snpsByOverlaps)
importFrom(BiocGenerics,path)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpstop)
importFrom(BiocParallel,bpworkers)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,vmatchPattern)
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,mapToTranscripts)
importFrom(GenomicRanges,GRanges)
importFrom(IRanges,IRanges)
importFrom(IRanges,extractList)
importFrom(IRanges,subsetByOverlaps)
importFrom(Matrix,colSums)
importFrom(Matrix,sparseMatrix)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,FaFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,index)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsamtools,scanFa)
importFrom(Rsamtools,scanFaIndex)
importFrom(Rsamtools,seqinfo)
importFrom(S4Vectors,aggregate)
importFrom(S4Vectors,unstrsplit)
importFrom(Seqinfo,Seqinfo)
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqlevels)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(rtracklayer,export)
importFrom(stats,model.matrix)
importFrom(stats,pbeta)
importFrom(utils,read.table)
importFrom(utils,write.table)
useDynLib(raer, .registration = TRUE)
