Index

A

aa_group_kmer (codonbias.stats.CodonCounter property)

B

BalancedWeight (class in codonbias.optimizers)

BaseCounter (class in codonbias.stats)

C

codon_base_idx_kmer (codonbias.stats.CodonCounter property) CodonAdaptationIndex (class in codonbias.scores) codonbias module codonbias.optimizers module codonbias.pairwise module codonbias.random module codonbias.scores module

codonbias.stats module codonbias.utils module CodonCounter (class in codonbias.stats) CodonPairBias (class in codonbias.scores) CodonUsageFrequency (class in codonbias.pairwise) count() (codonbias.stats.BaseCounter method) (codonbias.stats.CodonCounter method) count_array() (codonbias.stats.BaseCounter method) (codonbias.stats.CodonCounter method)

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) geomean_array() (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_permuted_seq() (codonbias.random.Permuter method) get_pval() (codonbias.random.Permuter method) get_score() (codonbias.pairwise.PairwiseScore method) (codonbias.scores.ScalarScore method)

get_table() (codonbias.stats.BaseCounter method) get_top_indices() (codonbias.utils.ReferenceSelector method) get_top_seqs() (codonbias.utils.ReferenceSelector method) get_vector() (codonbias.scores.VectorScore method) get_weights() (codonbias.scores.WeightScore method) get_zscore() (codonbias.random.Permuter method) greater_equal() (in module codonbias.utils)

I

IntraPosPermuter (class in codonbias.random)

IntraSeqPermuter (class in codonbias.random) iter_codons() (in module codonbias.utils)

K

kmer_index (codonbias.stats.BaseCounter property) (codonbias.stats.CodonCounter property)

L

less_equal() (in module codonbias.utils)

M

MaxWeight (class in codonbias.optimizers) mean() (in module codonbias.utils) mean_array() (in module codonbias.utils) MinWeight (class in codonbias.optimizers) module codonbias codonbias.optimizers codonbias.pairwise codonbias.random codonbias.scores codonbias.stats codonbias.utils

N

NormalizedTranslationalEfficiency (class in codonbias.scores)

O

optimize() (codonbias.optimizers.WeightOptimizer method)

optimize_s_values() (codonbias.scores.TrnaAdaptationIndex method)

P

PairwiseScore (class in codonbias.pairwise)

Permuter (class in codonbias.random) process_GtRNAdb_table() (in module codonbias.utils)

R

rankdata() (in module codonbias.utils) ReferenceSelector (class in codonbias.utils)

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

S

ScalarScore (class in codonbias.scores)

Score (class in codonbias.scores)

T

translate() (in module codonbias.utils)

TrnaAdaptationIndex (class in codonbias.scores)

V

VectorScore (class in codonbias.scores)

W

WeightOptimizer (class in codonbias.optimizers)

WeightScore (class in codonbias.scores)