NAMESPACE

# Generated by roxygen2: do not edit by hand

export("%>%")
export(addQcColsToMeta)
export(addRleSummaryStats)
export(archiveDatabase)
export(autoAuditQcTable)
export(brentlabRnaSeqExperiment)
export(brentlabRnaSeqSet)
export(brentlabRnaSeqSetFromDatabase)
export(brentlabRnaSeqSetTransform)
export(calculateGeneWiseMedians)
export(calculateRLE)
export(coerceToDds)
export(connectToDatabase)
export(createEPTally)
export(createEnvPertSet_perturbed)
export(createEnvPertSet_titrationWT)
export(createEnvPert_epWT)
export(createExperimentSet)
export(createIgvBatchscript)
export(createInductionSetTally)
export(createNfCorePipelineSampleSheet)
export(createNinetyMinuteInduction_2016grant)
export(createNinetyMinuteInduction_2016grantWithDoubles)
export(createNinetyMinuteInduction_all)
export(createNinetyMinuteInduction_non2016grant)
export(createNovoalignPipelineSamplesheet)
export(create_partitions)
export(create_variant_explorer)
export(decomposeStatus2Bit)
export(estimateSizeFactorsByProtocol)
export(extractColData)
export(extractDesignMatrix)
export(filterWtByExperimentalLibdate_90min)
export(fltrLowReplicateParams)
export(geneGRanges)
export(getCapsuleImageSet)
export(getGeneNames)
export(getMetadata)
export(getRawCounts)
export(getRunNumberLeadingZero)
export(getTable)
export(getUserAuthToken)
export(htseq_libraryComplexity)
export(htseq_locusLog2cpm)
export(htseq_notAlignedTotalPercent)
export(htseq_proteinCodingTotal)
export(igv_script)
export(isNumeric)
export(is_integer64)
export(listTables)
export(localView)
export(locusCoverage)
export(moveNfCoFastqFiles)
export(novoalignPipelineQC)
export(parseComparatives)
export(parseNovoalignLog)
export(patchTable)
export(postCapsuleJpeg)
export(postCapsuleJpeg_batch)
export(postCounts)
export(postCountsToDatabase)
export(postFastqSheet)
export(postImageAnnotationsToDatabase)
export(postQcSheet)
export(postTable)
export(qaFilter)
export(rank_response_plot)
export(readHTSeqFile)
export(readInData)
export(removeLibdateByReplicate)
export(removeParameterEffects)
export(replicateByProtocolTally)
export(rleByReplicateGroup)
export(rlePlot)
export(rlePlotCompareEffectRemoved)
export(rleSummary)
export(rleTransform)
export(setPerturbedLociToZero)
export(snpeff_summary_to_long)
export(sort_rank_mean_expr)
export(splitProtocolGroups)
export(strandedScanBamParam)
export(testBamPath)
export(test_train_partition)
export(visualize)
exportClasses(VariantExplorer)
exportClasses(brentlabRnaSeqExperiment)
exportClasses(brentlabRnaSeqSet)
exportClasses(brentlabRnaSeqSetTransform)
exportMethods(coerceToDds)
exportMethods(createExperimentSet)
exportMethods(estimateSizeFactorsByProtocol)
exportMethods(extractColData)
exportMethods(extractDesignMatrix)
exportMethods(qaFilter)
exportMethods(replicateByProtocolTally)
exportMethods(splitProtocolGroups)
exportMethods(summary)
exportMethods(test_train_partition)
exportMethods(visualize)
import(DESeq2)
import(dplyr)
import(foreach)
import(ggplot2)
import(magrittr)
import(methods)
import(tibble)
importClassesFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,sizeFactors)
importFrom(GenomicRanges,width)
importFrom(Gviz,AlignmentsTrack)
importFrom(Gviz,AnnotationTrack)
importFrom(Gviz,GenomeAxisTrack)
importFrom(Gviz,SequenceTrack)
importFrom(Gviz,plotTracks)
importFrom(RPostgres,Postgres)
importFrom(RPostgres,dbConnect)
importFrom(RPostgres,dbDisconnect)
importFrom(RPostgres,dbGetQuery)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,PileupParam)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,pileup)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,SimpleList)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,cbind)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(doParallel,registerDoParallel)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,coalesce)
importFrom(dplyr,collect)
importFrom(dplyr,distinct)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,mutate_if)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,rename_with)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarize)
importFrom(dplyr,tally)
importFrom(dplyr,tbl)
importFrom(edgeR,cpm)
importFrom(generics,visualize)
importFrom(httr,GET)
importFrom(httr,PATCH)
importFrom(httr,POST)
importFrom(httr,add_headers)
importFrom(httr,content)
importFrom(httr,content_type)
importFrom(httr,http_status)
importFrom(httr,status_code)
importFrom(httr,upload_file)
importFrom(iterators,iter)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(magrittr,"%>%")
importFrom(matrixStats,iqr)
importFrom(openxlsx,write.xlsx)
importFrom(parallel,makeForkCluster)
importFrom(parallel,stopCluster)
importFrom(purrr,map)
importFrom(readr,read_csv)
importFrom(readr,read_tsv)
importFrom(readr,write_csv)
importFrom(readxl,read_excel)
importFrom(rlang,is_formula)
importFrom(rlang,sym)
importFrom(stats,coef)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stringr,regex)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_remove)
importFrom(stringr,str_remove_all)
importFrom(stringr,str_replace)
importFrom(stringr,str_split)
importFrom(stringr,str_trim)
importFrom(tibble,as_tibble)
importFrom(tidyr,as_tibble)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyr,unite)
importFrom(utils,head)
importFrom(withr,local_options)