# Generated by roxygen2: do not edit by hand

export(bulk_long_pipeline)
export(bulk_windows_pipeline_setup)
export(create_config)
export(create_sce_from_dir)
export(create_se_from_dir)
export(get_default_config_file)
export(gff3_to_bed12)
export(match_cell_barcode_cpp)
export(merge_bulk_fastq)
export(merge_bulk_fastq_python)
export(parse_gff_tree)
export(parse_json_config)
export(samtools_as_bam)
export(samtools_sort_index)
export(sc_DTU_analysis)
export(sc_annotate_umap)
export(sc_long_multisample_pipeline)
export(sc_long_pipeline)
export(sc_mutations)
export(sc_windows_pipeline_setup)
export(windows_pipeline_isoforms)
export(windows_pipeline_quantification)
import(zlibbioc)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,start)
importFrom(ComplexHeatmap,AnnotationFunction)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(Matrix,colSums)
importFrom(Matrix,t)
importFrom(Matrix,tail)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,asBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,sortBam)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,head)
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(basilisk,BasiliskEnvironment)
importFrom(basilisk,basiliskRun)
importFrom(basilisk,basiliskStart)
importFrom(basilisk,basiliskStop)
importFrom(circlize,colorRamp2)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(dplyr,expr)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,groups)
importFrom(dplyr,left_join)
importFrom(dplyr,slice_max)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_at)
importFrom(dplyr,top_n)
importFrom(ggbio,autoplot)
importFrom(ggbio,geom_alignment)
importFrom(ggbio,xlim)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_colour_gradient2)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(grid,unit)
importFrom(grid,viewport)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,as_adjacency_matrix)
importFrom(magrittr,"%>%")
importFrom(reticulate,dict)
importFrom(reticulate,import_from_path)
importFrom(rtracklayer,import)
importFrom(rtracklayer,import.gff3)
importFrom(scater,runUMAP)
importFrom(scran,buildSNNGraph)
importFrom(scran,fixedPCA)
importFrom(scran,getTopHVGs)
importFrom(scran,modelGeneVar)
importFrom(scuttle,addPerCellQC)
importFrom(scuttle,addPerFeatureQC)
importFrom(scuttle,isOutlier)
importFrom(scuttle,logNormCounts)
importFrom(stats,chisq.test)
importFrom(stats,median)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_wider)
importFrom(utils,file_test)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.csv)
useDynLib(FLAMES, .registration=TRUE)
