Index

C

calc_neutral_mixing_rates() (gpmap.randwalk.WMWalk method)

calc_rate_matrix() (gpmap.randwalk.WMWalk method) calc_visualization() (gpmap.randwalk.WMWalk method)

D

DataSet (class in gpmap.datasets)

DiscreteSpace (class in gpmap.space)

F

figure_allele_grid() (in module gpmap.plot.ds) (in module gpmap.plot.mpl) figure_Ns_grid() (in module gpmap.plot.mpl)

fit() (gpmap.inference.MinimumEpistasisRegression method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method)

G

generate_freq_reduced_code() (in module gpmap.seq) get_alphabet() (in module gpmap.seq) get_custom_codon_table() (in module gpmap.seq) get_genotypes_from_region() (in module gpmap.genotypes) get_neighbor_pairs() (gpmap.space.DiscreteSpace method)

get_neighbors() (gpmap.space.DiscreteSpace method), [1] get_one_hot_from_alleles() (in module gpmap.seq) get_single_mutant_matrix() (gpmap.space.SequenceSpace method) get_state_idxs() (gpmap.space.DiscreteSpace method) GridSpace (class in gpmap.space) guess_space_configuration() (in module gpmap.seq)

H

HammingBallSpace (class in gpmap.space)

L

list_available_datasets() (in module gpmap.datasets)

M

make_contrasts() (gpmap.inference.MinimumEpistasisRegression method) (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method)

marginalize_landscape_positions() (in module gpmap.genotypes) MinimumEpistasisInterpolator (class in gpmap.inference) MinimumEpistasisRegression (class in gpmap.inference) msa_to_counts() (in module gpmap.seq)

P

plot_edges() (in module gpmap.plot.mpl) plot_nodes() (in module gpmap.plot.mpl) plot_relaxation_times() (in module gpmap.plot.mpl) plot_SeqDEFT_summary() (in module gpmap.plot.mpl) plot_visualization() (in module gpmap.plot.ds) (in module gpmap.plot.mpl) (in module gpmap.plot.ply)

predict() (gpmap.inference.MinimumEpistasisInterpolator method) (gpmap.inference.VCregression method) ProductSpace (class in gpmap.space)

R

read_dataframe() (in module gpmap.utils)

read_edges() (in module gpmap.utils) remove_codon_incompatible_transitions() (gpmap.space.SequenceSpace method)

S

select_genotypes() (in module gpmap.genotypes) SeqDEFT (class in gpmap.inference) SequenceSpace (class in gpmap.space)

simulate() (gpmap.inference.SeqDEFT method) (gpmap.inference.VCregression method) simulate_phi() (gpmap.inference.SeqDEFT method)

T

to_nucleotide_space() (gpmap.space.SequenceSpace method)

transcribe_seqs() (in module gpmap.seq) translate_seqs() (in module gpmap.seq)

V

VCregression (class in gpmap.inference)

W

WMWalk (class in gpmap.randwalk)

write_tables() (gpmap.randwalk.WMWalk method)