# Generated by roxygen2: do not edit by hand

export("config<-")
export("controllers<-")
export("steps<-")
export(BulkPipeline)
export(MultiSampleSCPipeline)
export(SingleCellPipeline)
export(add_gene_counts)
export(annotation_to_fasta)
export(barcode_group)
export(barcode_segment)
export(blaze)
export(bulk_long_pipeline)
export(combine_sce)
export(config)
export(controllers)
export(convolution_filter)
export(create_config)
export(create_sce_from_dir)
export(create_se_from_dir)
export(create_spe)
export(cutadapt)
export(demultiplex_sockeye)
export(example_pipeline)
export(experiment)
export(filter_annotation)
export(filter_coverage)
export(find_barcode)
export(find_bin)
export(find_diversity)
export(find_variants)
export(flexiplex)
export(get_coverage)
export(index_genome)
export(load_config)
export(mutation_positions)
export(plot_coverage)
export(plot_demultiplex)
export(plot_demultiplex_raw)
export(plot_durations)
export(plot_isoform_heatmap)
export(plot_isoform_reduced_dim)
export(plot_isoforms)
export(plot_spatial_feature)
export(plot_spatial_isoform)
export(resume_FLAMES)
export(run_FLAMES)
export(run_step)
export(sc_DTU_analysis)
export(sc_genotype)
export(sc_impute_transcript)
export(sc_long_multisample_pipeline)
export(sc_long_pipeline)
export(sc_mutations)
export(sc_plot_genotype)
export(steps)
export(weight_transcripts)
exportMethods("config<-")
exportMethods("controllers<-")
exportMethods("steps<-")
exportMethods(config)
exportMethods(controllers)
exportMethods(experiment)
exportMethods(index_genome)
exportMethods(plot_demultiplex)
exportMethods(plot_durations)
exportMethods(resume_FLAMES)
exportMethods(run_FLAMES)
exportMethods(run_step)
exportMethods(show)
exportMethods(steps)
importFrom(BiocGenerics,`%in%`)
importFrom(BiocGenerics,cbind)
importFrom(BiocGenerics,colnames)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,rownames)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,t)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,writeXStringSet)
importFrom(ComplexHeatmap,AnnotationFunction)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,seqnames)
importFrom(GenomicFeatures,extractTranscriptSeqs)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,coverage)
importFrom(GenomicRanges,disjoin)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,gaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,end)
importFrom(IRanges,start)
importFrom(IRanges,width)
importFrom(Matrix,readMM)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,tail)
importFrom(MatrixGenerics,rowSums)
importFrom(R.utils,gunzip)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,PileupParam)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,indexFa)
importFrom(Rsamtools,pileup)
importFrom(Rsamtools,quickBamFlagSummary)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,sortBam)
importFrom(S4Arrays,colsum)
importFrom(S4Arrays,rowsum)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,split)
importFrom(S4Vectors,subjectHits)
importFrom(Seqinfo,seqinfo)
importFrom(Seqinfo,seqlengths)
importFrom(Seqinfo,seqnames)
importFrom(ShortRead,readFastq)
importFrom(ShortRead,writeFastq)
importFrom(SingleCellExperiment,"altExp<-")
importFrom(SingleCellExperiment,"counts<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,altExp)
importFrom(SingleCellExperiment,altExpNames)
importFrom(SingleCellExperiment,altExps)
importFrom(SingleCellExperiment,colLabels)
importFrom(SingleCellExperiment,counts)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SingleCellExperiment,rowData)
importFrom(SpatialExperiment,"imgData<-")
importFrom(SpatialExperiment,SpatialExperiment)
importFrom(SpatialExperiment,imgData)
importFrom(SpatialExperiment,readImgData)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(abind,abind)
importFrom(bambu,bambu)
importFrom(bambu,prepareAnnotations)
importFrom(bambu,writeToGTF)
importFrom(basilisk,BasiliskEnvironment)
importFrom(basilisk,basiliskRun)
importFrom(basilisk,obtainEnvironmentPath)
importFrom(circlize,colorRamp2)
importFrom(cli,cli_alert)
importFrom(cli,cli_alert_danger)
importFrom(cli,cli_alert_info)
importFrom(cli,cli_alert_success)
importFrom(cli,cli_alert_warning)
importFrom(cli,cli_bullets)
importFrom(cli,cli_h3)
importFrom(cli,cli_rule)
importFrom(cli,cli_text)
importFrom(cowplot,plot_grid)
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,c_across)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,pull)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_at)
importFrom(dplyr,ungroup)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotation_raster)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,position_stack)
importFrom(ggplot2,scale_colour_gradient2)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(grDevices,as.raster)
importFrom(grid,arrow)
importFrom(grid,unit)
importFrom(grid,viewport)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,as_adjacency_matrix)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(magick,image_colorize)
importFrom(magick,image_read)
importFrom(magrittr,equals)
importFrom(methods,is)
importFrom(methods,show)
importFrom(readr,col_character)
importFrom(readr,col_integer)
importFrom(readr,col_logical)
importFrom(readr,read_delim)
importFrom(readr,read_table)
importFrom(reticulate,dict)
importFrom(reticulate,import_from_path)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import)
importFrom(scater,runPCA)
importFrom(scater,runUMAP)
importFrom(scatterpie,geom_scatterpie)
importFrom(scran,buildSNNGraph)
importFrom(scrapper,centerSizeFactors)
importFrom(scrapper,normalizeCounts)
importFrom(scrapper,normalizeRnaCounts.se)
importFrom(stats,convolve)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,weighted.mean)
importFrom(stringr,str_escape)
importFrom(stringr,str_split)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tidyr,as_tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyselect,matches)
importFrom(utils,file_test)
importFrom(utils,modifyList)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,write.table)
importFrom(withr,with_package)
importFrom(withr,with_path)
useDynLib(FLAMES, .registration=TRUE)
