[,codonTable-method     Subset 'codonTable' object.
Bplot                   Karlin B plot
codonTable-class        An S4 class 'codonTable'
codonUsage              Calculate CU measures.
codonUsage-expressivity
                        Calculate CU expressivity measures.
coRdon                  coRdon: codon usage analysis in R
crossTab-class          An S4 class 'crossTab'
enrichBarplot           Barplot of enriched and depleted annotations.
enrichMAplot            MA plot of enriched annotations.
enrichMatrix            Extract chosen enrichment values to a matrix.
enrichment              Enrichment analysis for codon usage (CU) data.
genCode-class           An S4 class 'genCode'
HD59                    Codon usage in healthy human gut microbiome.
HD59_KO                 Codon usage based KO enrichment analysis
                        results from the healthy human gut microbiome.
                        For more information, see '?HD59'.
HD59_PATHWAYS           Codon usage based KEGG Pathway enrichment
                        analysis results from a healthy human gut
                        microbiome. For more information, see '?HD59'.
intraBplot              Intra-samples Karlin B plot
LD94                    Codon usage in human gut microbiome in liver
                        cirrhosis.
LD94_KO                 Codon usage based KO enrichment analysis
                        results from an gut microbiome of an individual
                        with liver cirrhosis. For more information, see
                        '?LD94'.
LD94_PATHWAYS           Codon usage based KEGG Pathway enrichment
                        analysis results from an gut microbiome of an
                        individual with liver cirrhosis. For more
                        information, see '?LD94'.
length-codonTable       Length of 'codonTable' object.
length-crossTab         Length of 'crossTab' object.
readSet                 Read set of sequences.
reduceCrossTab          Reduce 'crossTab'.
RPKOs                   KEGG Orthology (KO) annotations for ribosomal
                        genes.
show-codonTable         Display the object of 'codonTable' class.
show-crossTab           Display the object of 'crossTab' class.
