FASTASummary-class      'FASTASummary' class representing the summaries
                        of a FASTA file
FASTQSummary-class      'FASTQSummary' class representing the summaries
                        of a FASTQ file
SequenceSummary-class   'SequenceSummary' class representing the
                        summaries of a sequence file
basePlot-methods        Plot Base Frequency or Proportion by Position
calcKL                  Calculate the Kullback-Leibler Divergence
                        Between the k-mer Distribution by Position and
                        the k-mer Distribution Across All Positions.
gcPlot-methods          Plot GC Content by Position
geom_qlinerange         Use Line Segments and Points to Plot Quality
                        Statistics by Position in the Read
getBase-methods         Get a Data Frame of Base Frequency Data from a
                        'SequenceSummary' Object
getBaseProp-methods     Get a Data Frame of Base Proportion Data from a
                        'SequenceSummary' object
getGC-methods           Get a Data Frame of GC Content from a
                        'SequenceSummary' object
getKmer-methods         Get a Data Frame of k-mer Frequency by Position
                        from a 'SequenceSummary' Object
getMCQual-methods       Get a Data Frame of Simulated Qualitied from a
                        'FASTQSummary' object
getQual-methods         Get a Data Frame of Quality Data from a
                        'FASTQSummary' object
getSeqlen-methods       Get a Data Frame of Sequence Lengths from a
                        'SequenceSummary' object
kmerEntropyPlot-methods
                        Plot Entropy of k-mers by Position
kmerKLPlot-methods      Plot K-L Divergence Components for a Subset of
                        k-mers to Inspect for Contamination
list2df                 Apply a function to items in list and combine
                        into data frame
makeReport-methods      Make an HTML report from a FASTASummary of
                        FASTQSummary object
plotBases-methods       Plot Bases by Position
plotGC-methods          Plot per Base GC Content by Position
plotQuals-methods       Plot a Base Quality Boxplot by Position
plotSeqLengths-methods
                        Plot Histogram of Sequence Lengths
qualPlot-methods        Plot a Base Quality Boxplot by Position
readSeqFile             Read and Summarize a Sequence (FASTA or FASTQ)
                        File
scale_color_dna         Set the color scheme to 'biovizBase"s for DNA
scale_color_iupac       Set the color scheme to 'biovizBase"s for IUPAC
                        codes
seqlenPlot-methods      Plot a Histogram of Sequence Lengths
