Bplot                   Karlin B plot
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'.
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'.
RPKOs                   KEGG Orthology (KO) annotations for ribosomal
                        genes.
[,codonTable-method     Subset 'codonTable' object.
coRdon                  coRdon: codon usage analysis in R
codonTable-class        An S4 class 'codonTable'
codonUsage              Calculate CU measures.
codonUsage-expressivity
                        Calculate CU expressivity measures.
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'
intraBplot              Intra-samples Karlin B plot
length-codonTable       Length of 'codonTable' object.
length-crossTab         Length of 'crossTab' object.
readSet                 Read set of sequences.
reduceCrossTab          Reduce 'crossTab'.
show-codonTable         Display the object of 'codonTable' class.
show-crossTab           Display the object of 'crossTab' class.
