CorMut-package |
Detect the correlated mutations based on selection pressure |
biCkaksAA |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biCkaksAA-class |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biCkaksCodon |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biCkaksCodon-class |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biCompare |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare-class |
Class "biCompare" |
biCompare-method |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare-methods |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare.biCkaksAA |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare.biCkaksCodon |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare.biJIAA |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare.biMIAA |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biCompare.biMICodon |
biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network |
biJIAA |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biJIAA-class |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biMIAA |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biMIAA-class |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biMICodon |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
biMICodon-class |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
ckaks |
Class "ckaks" |
ckaks-class |
Class "ckaks" |
ckaks.CorMut |
Class "ckaks" |
ckaks.CorMut-method |
Class "ckaks" |
ckaksAA |
Compute the conditional kaks(conditional selection pressure) among amino mutations |
ckaksCodon |
Compute the conditional kaks(conditional selection pressure) among codons |
CorMut |
Detect the correlated mutations based on selection pressure |
filterSites |
filterSites methods |
filterSites-method |
filterSites methods |
filterSites-methods |
filterSites methods |
filterSites.ckaks |
filterSites methods |
filterSites.JI |
filterSites methods |
filterSites.kaksAA |
filterSites methods |
filterSites.kaksCodon |
filterSites methods |
filterSites.MI |
filterSites methods |
JI-class |
Class "JI" |
ji.CorMut-method |
Class "JI" |
jiAA |
Compute the Jaccard index among individual amino mutations |
ka.CorMut |
Class "kaksAA" |
ka.CorMut-method |
Class "kaksAA" |
ka.CorMut-method |
Class "kaksCodon" |
kaks.CorMut |
Class "kaksAA" |
kaks.CorMut-method |
Class "kaksAA" |
kaks.CorMut-method |
Class "kaksCodon" |
kaksAA |
Compute kaks for individual amino mutation |
kaksAA-class |
Class "kaksAA" |
kaksCodon |
Compute kaks for individual codon |
kaksCodon-class |
Class "kaksCodon" |
ks.CorMut |
Class "kaksAA" |
ks.CorMut-method |
Class "kaksAA" |
ks.CorMut-method |
Class "kaksCodon" |
lod.CorMut |
Class "ckaks" |
lod.CorMut-method |
Class "ckaks" |
lod.CorMut-method |
Class "kaksAA" |
lod.CorMut-method |
Class "kaksCodon" |
method.CorMut |
Class "biCompare" |
method.CorMut-method |
Class "biCompare" |
MI-class |
Class "MI" |
mi.CorMut |
Class "MI" |
mi.CorMut-method |
Class "MI" |
miAA |
Compute the mutual information among individual amino mutations |
miCodon |
Compute the mutual information among codons |
p.value.CorMut |
Class "MI" |
p.value.CorMut-method |
Class "JI" |
p.value.CorMut-method |
Class "MI" |
plot |
Plot methods for CorMut package |
plot-method |
Plot methods for CorMut package |
plot.biCompare |
Plot methods for CorMut package |
plot.ckaks |
Plot methods for CorMut package |
plot.JI |
Plot methods for CorMut package |
plot.MI |
Plot methods for CorMut package |
positiveSite01.CorMut |
Class "biCompare" |
positiveSite01.CorMut-method |
Class "biCompare" |
positiveSite02.CorMut |
Class "biCompare" |
positiveSite02.CorMut-method |
Class "biCompare" |
q.CorMut |
Class "kaksAA" |
q.CorMut-method |
Class "kaksAA" |
q.CorMut-method |
Class "kaksCodon" |
seqFormat |
Process the multiple sequence alignment files |
seqFormat-methods |
Process the multiple sequence alignment files |
seq_num.CorMut |
Class "kaksAA" |
seq_num.CorMut-method |
Class "kaksAA" |
seq_num.CorMut-method |
Class "kaksCodon" |
show-method |
Class "JI" |
show-method |
Class "MI" |
show-method |
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA" |
show-method |
Class "ckaks" |
show-method |
Class "kaksAA" |
show-method |
Class "kaksCodon" |
state_1.CorMut |
Class "biCompare" |
state_1.CorMut-method |
Class "biCompare" |
state_2.CorMut |
Class "biCompare" |
state_2.CorMut-method |
Class "biCompare" |
statistic_1.CorMut |
Class "biCompare" |
statistic_1.CorMut-method |
Class "biCompare" |
statistic_2.CorMut |
Class "biCompare" |
statistic_2.CorMut-method |
Class "biCompare" |