Codon Usage Analysis and Prediction of Gene Expressivity

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Documentation for package ‘coRdon’ version 1.25.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.