Main functions
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createCountTableFromFastQs()
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Create sequence-based count tables |
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mergeAndAggregate()
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Aggregates sequence counts for each sequence cluster |
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runDESeq2()
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Run differential expression analysis based on DESeq2 |
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getConditionCountStats()
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Compute mean and standard deviation of normalized counts for each condition |
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createMap()
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Create a mapping of sequences to sequence identifiers |
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sequencesAsFasta()
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Create a vector of sequence identifiers and sequences in FASTA format |
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runBlast()
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Run BLAST for small RNA sequences |
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runClustering()
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Run CD-HIT clustering |
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mergeSingleAndClusterResults()
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Merges clustering results as well as DE results for single sequence and cluster approach |
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mergeResults()
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Merge intermediate results of DEUS |
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addCountsOfFeatureClasses()
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Count occurrences of feature classes |
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writeSummaryFiles()
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Write summary tables for DEUS result |
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getNoBlastHitFraction()
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Compute fraction of reads without BLAST hit for each sample |
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printClusterSummary()
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Prints a summary of the number of significant sequences and clusters |