QC for brentlab RNAseq data

Global functions
%>%	Man page
VariantExplorer-class	Man page
addQcColsToMeta	Man page Source code
addRleSummaryStats	Man page
archiveDatabase	Man page
autoAuditQcTable	Man page Source code
brentlabRnaSeqExperiment	Man page Source code
brentlabRnaSeqExperiment-class	Man page
brentlabRnaSeqSet	Man page Source code
brentlabRnaSeqSet-class	Man page
brentlabRnaSeqSetFromDatabase	Man page Source code
brentlabRnaSeqSetTransform	Man page Source code
brentlabRnaSeqSetTransform-class	Man page
calculateGeneWiseMedians	Man page
calculateRLE	Man page
coerceToDds	Man page
coerceToDds,brentlabRnaSeqSet-method	Man page
connectToDatabase	Man page Source code
createEPTally	Man page Source code
createEnvPertSet_perturbed	Man page Source code
createEnvPertSet_titrationWT	Man page Source code
createEnvPert_epWT	Man page Source code
createExperimentSet	Man page
createExperimentSet,brentlabRnaSeqSet-method	Man page
createIgvBatchscript	Man page Source code
createInductionSetTally	Man page Source code
createNfCorePipelineSampleSheet	Man page Source code
createNinetyMinuteInduction_2016grant	Man page Source code
createNinetyMinuteInduction_2016grantWithDoubles	Man page Source code
createNinetyMinuteInduction_all	Man page Source code
createNinetyMinuteInduction_non2016grant	Man page Source code
createNovoalignPipelineSamplesheet	Man page Source code
create_partitions	Man page Source code
create_variant_explorer	Man page Source code
database_colnames	Man page
database_info	Man page
decomposeStatus2Bit	Man page Source code
estimateSizeFactorsByProtocol	Man page
estimateSizeFactorsByProtocol,brentlabRnaSeqExperiment-method	Man page
extractColData	Man page
extractColData,brentlabRnaSeqSet-method	Man page
extractDesignMatrix	Man page
extractDesignMatrix,brentlabRnaSeqSet-method	Man page
filterWtByExperimentalLibdate_90min	Man page Source code
fltrLowReplicateParams	Man page Source code
geneGRanges	Man page Source code
getCapsuleImageSet	Man page
getGeneNames	Man page
getMetadata	Man page Source code
getRawCounts	Man page
getRunNumberLeadingZero	Man page Source code
getTable	Man page
getUserAuthToken	Man page
grant_df	Man page
htseq_libraryComplexity	Man page Source code
htseq_locusLog2cpm	Man page Source code
htseq_notAlignedTotalPercent	Man page Source code
htseq_proteinCodingTotal	Man page Source code
igv_script	Man page
igv_script,VariantExplorer-method	Man page
isNumeric	Man page
is_integer64	Man page Source code
kn99_novo_htseq_status	Man page
kn99_novo_htseq_thresholds	Man page
listTables	Man page
localView	Man page Source code
locusCoverage	Man page Source code
moveNfCoFastqFiles	Man page Source code
novoalignPipelineQC	Man page Source code
parseComparatives	Man page Source code
parseNovoalignLog	Man page Source code
passing_genes_all	Man page
patchTable	Man page
plotRLEhistograms	Man page
postCapsuleJpeg	Man page
postCapsuleJpeg_batch	Man page
postCounts	Man page
postCountsToDatabase	Man page
postFastqSheet	Man page
postImageAnnotationsToDatabase	Man page
postQcSheet	Man page
postTable	Man page
qaFilter	Man page
qaFilter,brentlabRnaSeqExperiment-method	Man page
qaFilter,brentlabRnaSeqSet-method	Man page
rank_response_plot	Man page Source code
readHTSeqFile	Man page
readInData	Man page Source code
reexports	Man page
removeLibdateByReplicate	Man page
removeParameterEffects	Man page Source code
replicateByProtocolTally	Man page
replicateByProtocolTally,brentlabRnaSeqExperiment-method	Man page
replicateByProtocolTally_90min	Man page Source code
rleByReplicateGroup	Man page
rlePlot	Man page
rlePlotCompareEffectRemoved	Man page
rlePlot_helper	Man page
rleSummary	Man page
rleTransform	Man page Source code
run_numbers_with_leading_zero	Man page
setPerturbedLociToZero	Man page Source code
snpeff_summary_to_long	Man page Source code
sort_rank_mean_expr	Man page Source code
splitProtocolGroups	Man page
splitProtocolGroups,brentlabRnaSeqSet-method	Man page
strandedScanBamParam	Man page Source code
summary,VariantExplorer-method	Man page
testBamPath	Man page Source code
test_train_partition	Man page
test_train_partition,brentlabRnaSeqExperiment-method	Man page
visualize	Man page
visualize,VariantExplorer-method	Man page