Pipelines

• Pipeline bam_qc.py
• flatGeneset()
• collectRnaSeqMetrics()
• loadCollectRnaSeqMetrics()
• threePrimeBias()
• loadThreePrimeBias()
• estimateLibraryComplexity()
• loadEstimateLibraryComplexity()
• alignmentSummaryMetrics()
• loadAlignmentSummaryMetrics()
• insertSizeMetricsAndHistograms()
• loadInsertSizeMetrics()
• loadInsertSizeHistograms()
• fractionSpliced()
• loadFractionSpliced()
• loadSampleInformation()
• qcSummary()
• loadQCSummary()
• qc()
• pipeline_ensembl.py
• extractYPAR()
• hardMaskYPAR()
• contigs()
• filteredTranscriptFasta()
• filteredGTF()
• transcriptToGeneMap()
• transcriptInfo()
• full()
• Pipeline fastqc.py
• buildFastQCSummaryStatus()
• loadFastQC()
• loadMetadata()
• Pipeline feature_counts.py
• count()
• loadCounts()
• geneCounts()
• loadGeneCounts()
• loadTranscriptInfo()
• nGenesDetected()
• loadNGenesDetected()
• pipeline_hisat_index.py
• spliceSites()
• exons()
• transcriptomeIndex()
• full()
• Pipeline hisat.py
• firstPass()
• novelSpliceSites()
• secondPass()
• Pipeline preprocess_quantseq_fed
• cutadapt()
• pipeline_salmon_index.py
• index()
• full()
• Pipeline salmon.py
• quant()
• loadSalmonTranscriptQuant()
• loadSalmonGeneQuant()
• salmonTPMs()
• loadSalmonTPMs()
• tximeta()
• quantitation()
• loadTranscriptInfo()
• numberGenesDetected()
• loadNumberGenesDetected()