NAMESPACE

# Generated by roxygen2: do not edit by hand

export(create_kallisto_index)
export(download_fasta_intergenic)
export(download_kallisto)
export(generate_calls_workflow)
export(generate_presence_absence)
export(generate_slurm_calls)
export(generate_slurm_indexes)
export(getIntergenicPrefix)
export(getIntergenicRelease)
export(getRunIds)
export(getSimpleArborescence)
export(getWorkingPath)
export(get_summary_stats)
export(list_bgee_ref_intergenic_species)
export(list_community_ref_intergenic_species)
export(list_intergenic_release)
export(merge_transcriptome_and_intergenic)
export(merging_libraries)
export(run_kallisto)
export(run_tximport)
export(setAnnotationFromFile)
export(setAnnotationFromObject)
export(setIntergenicRelease)
export(setOutputDir)
export(setRNASeqLibPath)
export(setRunIds)
export(setSimpleArborescence)
export(setTranscriptomeFromFile)
export(setTranscriptomeFromObject)
export(setWorkingPath)
exportClasses(KallistoMetadata)
import(data.table)
import(jsonlite)
import(rhdf5)
import(rslurm)
import(rtracklayer)
import(sjmisc)
import(tximport)
importFrom(GenomicFeatures, makeTxDbFromGRanges)
importFrom(dplyr, filter)
importFrom(Biostrings, readDNAStringSet, writeXStringSet)
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "arrows", "axis", "legend", "lines", "par",
    "plot","mtext")
importFrom("methods", "callNextMethod", "is", "new", "validObject")
importFrom("stats", "density", "na.omit")
importFrom("utils", "compareVersion", "download.file",
    "packageVersion", "read.table", "untar", "unzip",
    "write.table")