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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(AddCellMetaToVDJ)
export(annotatePairing)
export(collapseBCR)
export(collapseIntoMetagenes)
export(combineBCR)
export(combineLoomFiles)
export(compareTransitionMatrices)
export(convertSeuratToH5ad)
export(fitTPT)
export(fitTransitionModel)
export(getCSRpotential)
export(getIGHmapping)
export(getIGHreadType)
export(getIsotype)
export(getSHM)
export(guessBarcodes)
export(mergeIgHCountsToSeurat)
export(mergeVelocytoWithGEX)
export(normalise_dimreduce)
export(plotFluxMatrix)
export(plotStationaryDistribution)
export(plot_arrows)
export(prepare_sciCSR)
export(read_loom_matrices)
export(repairBarcode)
export(run_scVelo)
export(scanBam)
export(splitAnnData)
export(summariseIGHreads)
import(Matrix)
import(Seurat)
import(ggplot2)
import(hdf5r)
import(markovchain)
import(reticulate)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomicAlignments,findOverlaps)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,flank)
importFrom(GenomicRanges,mcols)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,sort)
importFrom(GenomicRanges,start)
importFrom(IRanges,IRanges)
importFrom(Matrix,colSums)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,countQueryHits)
importFrom(Seurat,AddMetaData)
importFrom(Seurat,Assays)
importFrom(Seurat,Cells)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,ScaleData)
importFrom(cowplot,theme_cowplot)
importFrom(grid,grid.newpage)
importFrom(grid,grid.raster)
importFrom(harmony,RunHarmony)
importFrom(hdf5r,H5File)
importFrom(hdf5r,list.datasets)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,neighbors)
importFrom(methods,as)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(nnls,nnls)
importFrom(philentropy,JSD)
importFrom(philentropy,KL)
importFrom(plyr,ddply)
importFrom(png,readPNG)
importFrom(reshape2,acast)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(reticulate,py_config)
importFrom(reticulate,use_condaenv)
importFrom(sceasy,convertFormat)
importFrom(stats,as.formula)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_locate)
importFrom(stringr,str_replace)
importFrom(stringr,str_sub)
importFrom(stringr,str_to_lower)
importFrom(stringr,str_to_sentence)
importFrom(stringr,str_to_upper)