Index

C

CodonAdaptationIndex (class in codonbias.scores) codonbias module codonbias.pairwise module codonbias.scores module

codonbias.stats module codonbias.utils module CodonCounter (class in codonbias.stats) CodonUsageFrequency (class in codonbias.pairwise)

E

EffectiveNumberOfCodons (class in codonbias.scores)

F

fetch_GCN_from_GtRNAdb() (in module codonbias.utils)

FrequencyOfOptimalCodons (class in codonbias.scores)

G

geomean() (in module codonbias.utils) get_aa_table() (codonbias.stats.CodonCounter method) get_codon_table() (codonbias.stats.CodonCounter method) get_matrix() (codonbias.pairwise.PairwiseScore method)

get_score() (codonbias.pairwise.PairwiseScore method) (codonbias.scores.ScalarScore method) get_vector() (codonbias.scores.VectorScore method) get_weights() (codonbias.scores.RelativeSynonymousCodonUsage method)

M

mean() (in module codonbias.utils) module codonbias codonbias.pairwise codonbias.scores codonbias.stats codonbias.utils

P

PairwiseScore (class in codonbias.pairwise)

process_GtRNAdb_table() (in module codonbias.utils)

R

RelativeCodonBiasScore (class in codonbias.scores)

RelativeSynonymousCodonUsage (class in codonbias.scores) reverse_complement() (in module codonbias.utils)

S

ScalarScore (class in codonbias.scores)

T

TrnaAdaptationIndex (class in codonbias.scores)

V

VectorScore (class in codonbias.scores)