FastpData-class         The FastpData Object Class
FastpDataList-class     The FastpDataList Object Class
FastqcData-class        The FastqcData Object Class
FastqcDataList-class    The FastqcDataList Object Class
PwfCols-class           The PwfCols class and associated methods
TheoreticalGC-class     The TheoreticalGC Object Class
[,FastqcDataList,numeric,missing-method
                        Extract Elements
estGcDistn              Estimate a GC Content Distribution From
                        Sequences
fqName                  Return the Underlying Fastq File Names from
                        Fastqc/Fastp Objects
fqcVersion,FastqcData-method
                        Get the FASTQC version
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
mData                   Extract Metadata for TheoreticalGC objects
maxAdapterContent       Get the maximum Adapter Content
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
readTotals              Get the read totals
summariseOverrep        Summarise Overrepresented Sequences
writeHtmlReport         Write an HTML Summary Report
