## Main functions

createCountTableFromFastQs()

Create sequence-based count tables

mergeAndAggregate()

Aggregates sequence counts for each sequence cluster

runDESeq2()

Run differential expression analysis based on DESeq2

getConditionCountStats()

Compute mean and standard deviation of normalized counts for each condition

createMap()

Create a mapping of sequences to sequence identifiers

sequencesAsFasta()

Create a vector of sequence identifiers and sequences in FASTA format

runBlast()

Run BLAST for small RNA sequences

runClustering()

Run CD-HIT clustering

mergeSingleAndClusterResults()

Merges clustering results as well as DE results for single sequence and cluster approach

mergeResults()

Merge intermediate results of DEUS

addCountsOfFeatureClasses()

Count occurrences of feature classes

writeSummaryFiles()

Write summary tables for DEUS result

getNoBlastHitFraction()

Compute fraction of reads without BLAST hit for each sample

printClusterSummary()

Prints a summary of the number of significant sequences and clusters

## Internal functions

plotSampleDistanceMap()

Plot sample distance heatmap

plotPCA()

Plot result of PCA

processClusters()

Processes CD-HIT result file

printCluster()

Print FASTA file for cluster of sequences

deleteTmp()

Remove temporary FASTA file required for clustering