coRdon-package	coRdon
B	codonUsage
B,codonTable-method	codonUsage
Bplot	bplot
Bplot,character,character,matrix-method	bplot
Bplot,numeric,numeric,missing-method	bplot
CAI	codonUsage-expressivity
CAI,codonTable-method	codonUsage-expressivity
codonCounts	codonTable-class
codonCounts,codonTable-method	codonTable-class
codonTable	codonTable-class
codonTable,data.frame-method	codonTable-class
codonTable,DNAStringSet-method	codonTable-class
codonTable,matrix-method	codonTable-class
codonTable-class	codonTable-class
codonUsage	codonUsage
codonUsage-expressivity	codonUsage-expressivity
contable	crossTab-class
contable,crossTab-method	crossTab-class
coRdon	coRdon
crossTab	crossTab-class
crossTab,character,numeric-method	crossTab-class
crossTab-class	crossTab-class
E	codonUsage-expressivity
E,codonTable-method	codonUsage-expressivity
ENC	codonUsage
ENC,codonTable-method	codonUsage
ENCprime	codonUsage
ENCprime,codonTable-method	codonUsage
enrichBarplot	enrichBarplot
enrichBarplot,AnnotatedDataFrame-method	enrichBarplot
enrichBarplot,list-method	enrichBarplot
enrichMAplot	enrichMAplot
enrichMAplot,AnnotatedDataFrame-method	enrichMAplot
enrichMAplot,list-method	enrichMAplot
enrichMatrix	enrichMatrix
enrichMatrix,list-method	enrichMatrix
enrichment	enrichment
enrichment,crossTab-method	enrichment
Fop	codonUsage-expressivity
Fop,codonTable-method	codonUsage-expressivity
GCB	codonUsage-expressivity
GCB,codonTable-method	codonUsage-expressivity
genCode	genCode-class
genCode,ANY-method	genCode-class
genCode-class	genCode-class
getCOG	codonTable-class
getCOG,codonTable-method	codonTable-class
getID	codonTable-class
getID,codonTable-method	codonTable-class
getKO	codonTable-class
getKO,codonTable-method	codonTable-class
getlen	codonTable-class
getlen,codonTable-method	codonTable-class
getSeqAnnot	crossTab-class
getSeqAnnot,crossTab-method	crossTab-class
getVariable	crossTab-class
getVariable,crossTab-method	crossTab-class
HD59	HD59
HD59_KO	HD59_KO
HD59_PATHWAYS	HD59_PATHWAYS
intraBplot	intraBplot
intraBplot,codonTable,codonTable-method	intraBplot
LD94	LD94
LD94_KO	LD94_KO
LD94_PATHWAYS	LD94_PATHWAYS
length,codonTable-method	length-codonTable
length,crossTab-method	length-crossTab
length-codonTable	length-codonTable
length-crossTab	length-crossTab
MCB	codonUsage
MCB,codonTable-method	codonUsage
MELP	codonUsage-expressivity
MELP,codonTable-method	codonUsage-expressivity
MILC	codonUsage
MILC,codonTable-method	codonUsage
readSet	readSet
reduceCrossTab	reduceCrossTab
reduceCrossTab,crossTab,character-method	reduceCrossTab
RPKOs	RPKOs
SCUO	codonUsage
SCUO,codonTable-method	codonUsage
setCOG	codonTable-class
setCOG,codonTable-method	codonTable-class
setKO	codonTable-class
setKO,codonTable-method	codonTable-class
show,codonTable-method	show-codonTable
show,crossTab-method	show-crossTab
show-codonTable	show-codonTable
show-crossTab	show-crossTab
subset.codonTable	subset
[,codonTable-method	subset
[[,codonTable-method	subset
