[,FastqcDataList,numeric,missing-method
                        Extract Elements
estGcDistn              Estimate a GC Content Distribution From
                        Sequences
FastpData-class         The FastpData Object Class
FastpDataList-class     The FastpDataList Object Class
FastqcData-class        The FastqcData Object Class
FastqcDataList-class    The FastqcDataList Object Class
fqcVersion,FastqcData-method
                        Get the FASTQC version
fqName                  Return the Underlying Fastq File Names from
                        Fastqc/Fastp Objects
gcAvail                 List Genomes or Transcriptomes with Theoretical
                        GC Content
gcTheoretical           Theoretical GC content
getColours              Work with objects of class PwfCols
getGC                   Get Theoretical GC content
getModule,FastqcData-method
                        Retrieve a given module from a Fastqc* Object
getSummary,.FastqcFile-method
                        Get the summary information from Fastqc Files
importNgsLogs           Import Various NGS-related log files
importSJ                Import STAR Splice Junctions
isCompressed            Check to see if a file is compressed
maxAdapterContent       Get the maximum Adapter Content
mData                   Extract Metadata for TheoreticalGC objects
overRep2Fasta           Write fasta of Over-Represented sequences.
path                    Return the File Paths from an object
plotAdapterContent      Draw an Adapter Content Plot
plotAlignmentSummary    Plot a summary of alignments
plotAssemblyStats       Plot a summary of assembly logs
plotBaseQuals           Plot the Base Qualities for each file
plotDupLevels           Plot the combined Sequence_Duplication_Levels
                        information
plotFastqcPCA           Draw a PCA plot for Fast QC modules
plotGcContent           Plot the Per Sequence GC Content
plotInsertSize          Plot Insert Size Distributions
plotKmers               Plot Overrepresented Kmers
plotNContent            Draw an N Content Plot
plotOverrep             Plot a summary of Over-represented Sequences
plotReadTotals          Draw a barplot of read totals
plotSeqContent          Plot the per base content as a heatmap
plotSeqLengthDistn      Plot the Sequence Length Distribution
plotSeqQuals            Plot the Per Sequence Quality Scores
plotSummary             Plot the PASS/WARN/FAIL information
pwf                     Colours for PASS/WARN/FAIL
PwfCols-class           The PwfCols class and associated methods
readTotals              Get the read totals
summariseOverrep        Summarise Overrepresented Sequences
TheoreticalGC-class     The TheoreticalGC Object Class
writeHtmlReport         Write an HTML Summary Report
