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| estGcDistn | Estimate a GC Content Distribution From Sequences |
| estGcDistn-method | Estimate a GC Content Distribution From Sequences |
| FastqcData | The FastqcData Object Class |
| FastqcData-class | The FastqcData Object Class |
| FastqcDataList | The FastqcDataList Object Class |
| FastqcDataList-class | The FastqcDataList Object Class |
| fqcVersion | Get the FASTQC version |
| fqcVersion-method | Get the FASTQC version |
| fqName | Return the Underlying Fastq File Names from FastqcData* Objects |
| fqName-method | Return the Underlying Fastq File Names from FastqcData* Objects |
| fqName<- | Return the Underlying Fastq File Names from FastqcData* Objects |
| fqName<--method | Return the Underlying Fastq File Names from FastqcData* Objects |
| gcAvail | List Genomes or Transcriptomes with Theoretical GC Content |
| gcAvail-method | List Genomes or Transcriptomes with Theoretical GC Content |
| gcTheoretical | Theoretical GC content |
| getColours | Work with objects of class PwfCols |
| getColours-method | Work with objects of class PwfCols |
| getGC | Get Theoretical GC content |
| getGC-method | Get Theoretical GC content |
| getModule | Retrieve a given module from a Fastqc* Object |
| getModule-method | Retrieve a given module from a Fastqc* Object |
| getSummary | Get the summary information from Fastqc Files |
| getSummary-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 |
| mData-method | Extract Metadata for TheoreticalGC objects |
| overRep2Fasta | Write fasta of Over-Represented sequences. |
| overRep2Fasta-method | Write fasta of Over-Represented sequences. |
| path | Return the File Paths from an object |
| path-method | Return the File Paths from an object |
| plotAdapterContent | Draw an Adapter Content Plot |
| plotAdapterContent-method | 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 |
| plotBaseQuals-method | Plot the Base Qualities for each file |
| plotDupLevels | Plot the combined Sequence_Duplication_Levels information |
| plotDupLevels-method | Plot the combined Sequence_Duplication_Levels information |
| plotFastqcPCA | Draw a PCA plot for Fast QC modules |
| plotFastqcPCA-method | Draw a PCA plot for Fast QC modules |
| plotGcContent | Plot the Per Sequence GC Content |
| plotGcContent-method | Plot the Per Sequence GC Content |
| plotKmers | Plot Overrepresented Kmers |
| plotKmers-method | Plot Overrepresented Kmers |
| plotNContent | Draw an N Content Plot |
| plotNContent-method | Draw an N Content Plot |
| plotOverrep | Plot a summary of Over-represented Sequences |
| plotOverrep-method | Plot a summary of Over-represented Sequences |
| plotReadTotals | Draw a barplot of read totals |
| plotReadTotals-method | Draw a barplot of read totals |
| plotSeqContent | Plot the per base content as a heatmap |
| plotSeqContent-method | Plot the per base content as a heatmap |
| plotSeqLengthDistn | Plot the Sequence Length Distribution |
| plotSeqLengthDistn-method | Plot the Sequence Length Distribution |
| plotSeqQuals | Plot the Per Sequence Quality Scores |
| plotSeqQuals-method | Plot the Per Sequence Quality Scores |
| plotSummary | Plot the PASS/WARN/FAIL information |
| plotSummary-method | Plot the PASS/WARN/FAIL information |
| pwf | Colours for PASS/WARN/FAIL |
| PwfCols | The PwfCols class and associated methods |
| PwfCols-class | The PwfCols class and associated methods |
| readTotals | Get the read totals |
| runFastQC | Deprecated wrapper for the bash shell command fastqc. |
| runFastQC-method | Deprecated wrapper for the bash shell command fastqc. |
| setAlpha | Work with objects of class PwfCols |
| setAlpha-method | Work with objects of class PwfCols |
| setColours | Work with objects of class PwfCols |
| setColours-method | Work with objects of class PwfCols |
| TheoreticalGC-class | The TheoreticalGC Object Class |
| writeHtmlReport | Write an HTML Summary Report |
| [-method | Extract Elements |