![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| coRdon-package | coRdon: codon usage analysis in R |
| B | Calculate CU measures. |
| B-method | Calculate CU measures. |
| Bplot | Karlin B plot |
| Bplot-method | Karlin B plot |
| CAI | Calculate CU expressivity measures. |
| CAI-method | Calculate CU expressivity measures. |
| codonCounts | An S4 class 'codonTable' |
| codonCounts-method | An S4 class 'codonTable' |
| codonTable | An S4 class 'codonTable' |
| codonTable-class | An S4 class 'codonTable' |
| codonTable-method | An S4 class 'codonTable' |
| codonUsage | Calculate CU measures. |
| codonUsage-expressivity | Calculate CU expressivity measures. |
| contable | An S4 class 'crossTab' |
| contable-method | An S4 class 'crossTab' |
| coRdon | coRdon: codon usage analysis in R |
| crossTab | An S4 class 'crossTab' |
| crossTab-class | An S4 class 'crossTab' |
| crossTab-method | An S4 class 'crossTab' |
| E | Calculate CU expressivity measures. |
| E-method | Calculate CU expressivity measures. |
| ENC | Calculate CU measures. |
| ENC-method | Calculate CU measures. |
| ENCprime | Calculate CU measures. |
| ENCprime-method | Calculate CU measures. |
| enrichBarplot | Barplot of enriched and depleted annotations. |
| enrichBarplot-method | Barplot of enriched and depleted annotations. |
| enrichMAplot | MA plot of enriched annotations. |
| enrichMAplot-method | MA plot of enriched annotations. |
| enrichMatrix | Extract chosen enrichment values to a matrix. |
| enrichMatrix-method | Extract chosen enrichment values to a matrix. |
| enrichment | Enrichment analysis for codon usage (CU) data. |
| enrichment-method | Enrichment analysis for codon usage (CU) data. |
| Fop | Calculate CU expressivity measures. |
| Fop-method | Calculate CU expressivity measures. |
| GCB | Calculate CU expressivity measures. |
| GCB-method | Calculate CU expressivity measures. |
| genCode | An S4 class 'genCode' |
| genCode-class | An S4 class 'genCode' |
| genCode-method | An S4 class 'genCode' |
| getCOG | An S4 class 'codonTable' |
| getCOG-method | An S4 class 'codonTable' |
| getID | An S4 class 'codonTable' |
| getID-method | An S4 class 'codonTable' |
| getKO | An S4 class 'codonTable' |
| getKO-method | An S4 class 'codonTable' |
| getlen | An S4 class 'codonTable' |
| getlen-method | An S4 class 'codonTable' |
| getSeqAnnot | An S4 class 'crossTab' |
| getSeqAnnot-method | An S4 class 'crossTab' |
| getVariable | An S4 class 'crossTab' |
| getVariable-method | An S4 class 'crossTab' |
| 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 |
| intraBplot-method | 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. |
| length-method | Length of 'codonTable' object. |
| length-method | Length of 'crossTab' object. |
| MCB | Calculate CU measures. |
| MCB-method | Calculate CU measures. |
| MELP | Calculate CU expressivity measures. |
| MELP-method | Calculate CU expressivity measures. |
| MILC | Calculate CU measures. |
| MILC-method | Calculate CU measures. |
| readSet | Read set of sequences. |
| reduceCrossTab | Reduce 'crossTab'. |
| reduceCrossTab-method | Reduce 'crossTab'. |
| RPKOs | KEGG Orthology (KO) annotations for ribosomal genes. |
| SCUO | Calculate CU measures. |
| SCUO-method | Calculate CU measures. |
| setCOG | An S4 class 'codonTable' |
| setCOG-method | An S4 class 'codonTable' |
| setKO | An S4 class 'codonTable' |
| setKO-method | An S4 class 'codonTable' |
| show-codonTable | Display the object of 'codonTable' class. |
| show-crossTab | Display the object of 'crossTab' class. |
| show-method | Display the object of 'codonTable' class. |
| show-method | Display the object of 'crossTab' class. |
| subset.codonTable | Subset 'codonTable' object. |
| [-method | Subset 'codonTable' object. |
| [[-method | Subset 'codonTable' object. |