| FASTASummary-class | 'FASTASummary' class representing the summaries of a FASTA file |
| FASTQSummary-class | 'FASTQSummary' class representing the summaries of a FASTQ file |
| makeReport | Make an HTML report from a FASTASummary of FASTQSummary object |
| makeReport-method | 'FASTASummary' class representing the summaries of a FASTA file |
| makeReport-method | 'FASTQSummary' class representing the summaries of a FASTQ file |
| makeReport-methods | Make an HTML report from a FASTASummary of FASTQSummary object |
| plotBases | Plot Bases by Position |
| plotBases-method | 'SequenceSummary' class representing the summaries of a sequence file |
| plotBases-methods | Plot Bases by Position |
| plotGC | Plot per Base GC Content by Position |
| plotGC-method | 'SequenceSummary' class representing the summaries of a sequence file |
| plotGC-methods | Plot per Base GC Content by Position |
| plotQuals | Plot a Base Quality Boxplot by Position |
| plotQuals-method | 'FASTQSummary' class representing the summaries of a FASTQ file |
| plotQuals-methods | Plot a Base Quality Boxplot by Position |
| plotSeqLengths | Plot Histogram of Sequence Lengths |
| plotSeqLengths-method | 'SequenceSummary' class representing the summaries of a sequence file |
| plotSeqLengths-methods | Plot Histogram of Sequence Lengths |
| readSeqFile | Read and Summarize a Sequence (FASTA or FASTQ) File |
| SequenceSummary-class | 'SequenceSummary' class representing the summaries of a sequence file |