# Generated by roxygen2: do not edit by hand

export(bulk_long_pipeline)
export(bulk_windows_pipeline_setup)
export(create_config)
export(get_default_config_file)
export(gff3_to_bed12)
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_long_pipeline)
export(sc_mutations)
export(sc_windows_pipeline_setup)
export(windows_pipeline_isoforms)
export(windows_pipeline_quantification)
import(zlibbioc)
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(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(basilisk,BasiliskEnvironment)
importFrom(basilisk,basiliskRun)
importFrom(basilisk,basiliskStart)
importFrom(basilisk,basiliskStop)
importFrom(dplyr,expr)
importFrom(dplyr,group_by)
importFrom(dplyr,groups)
importFrom(dplyr,left_join)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_at)
importFrom(dplyr,top_n)
importFrom(magrittr,"%>%")
importFrom(reticulate,dict)
importFrom(reticulate,import_from_path)
importFrom(scater,runUMAP)
importFrom(scuttle,addPerCellQC)
importFrom(scuttle,addPerFeatureQC)
importFrom(scuttle,isOutlier)
importFrom(stats,chisq.test)
importFrom(stats,p.adjust)
importFrom(tidyr,gather)
importFrom(tidyr,pivot_wider)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,write.csv)
useDynLib(FLAMES, .registration=TRUE)
