Index _ | A | B | C | D | E | F | I | K | L | M | N | O | P | Q | R | S | T | U | W _ __init__() (chamois.classyfire.Cache method) (chamois.classyfire.Classification method) (chamois.domains.PfamAnnotator method) (chamois.model.ClusterSequence method) (chamois.model.Domain method) (chamois.model.PfamDomain method) (chamois.model.Protein method) (chamois.orf.CDSFinder method) (chamois.orf.PyrodigalFinder method) (chamois.predictor.ChemicalOntologyPredictor method) _leaves_to_root() (chamois.ontology.AdjacencyMatrix method) _roots_to_leaves() (chamois.ontology.AdjacencyMatrix method) A accession (chamois.model.Domain attribute) (chamois.model.PfamDomain attribute) adjacency_matrix (chamois.ontology.Ontology attribute) AdjacencyMatrix (class in chamois.ontology) ancestors() (chamois.ontology.AdjacencyMatrix method) annotate_domains() (chamois.domains.DomainAnnotator method) (chamois.domains.PfamAnnotator method) B binarize_classification() (in module chamois.classyfire) build_compositions() (in module chamois.compositions) build_observations() (in module chamois.compositions) build_variables() (in module chamois.compositions) C Cache (class in chamois.classyfire) CDSFinder (class in chamois.orf) chamois.classyfire module chamois.compositions module chamois.domains module chamois.model module chamois.ontology module chamois.orf module chamois.predictor module chamois.predictor.information module checksum() (chamois.predictor.ChemicalOntologyPredictor method) ChemicalOntologyPredictor (class in chamois.predictor) children() (chamois.ontology.AdjacencyMatrix method) Classification (class in chamois.classyfire) client (chamois.classyfire.Query attribute) Client (class in chamois.classyfire) cluster (chamois.model.Protein attribute) ClusterSequence (class in chamois.model) D descendants() (chamois.ontology.AdjacencyMatrix method) description (chamois.model.Domain attribute) (chamois.model.PfamDomain attribute) disentangle_domains() (chamois.domains.PfamAnnotator method) Domain (class in chamois.model) DomainAnnotator (class in chamois.domains) E end (chamois.model.PfamDomain attribute) evalue (chamois.model.PfamDomain attribute) F fetch() (chamois.classyfire.Client method) find_genes() (chamois.orf.CDSFinder method) (chamois.orf.ORFFinder method) (chamois.orf.PyrodigalFinder method) fit() (chamois.predictor.ChemicalOntologyPredictor method) folder (chamois.classyfire.Cache attribute) from_dict() (chamois.classyfire.Classification class method) (chamois.classyfire.Term class method) I id (chamois.classyfire.Query attribute) (chamois.model.ClusterSequence property) (chamois.model.Protein attribute) IncompleteGeneWarning (class in chamois.orf) information_accretion() (in module chamois.predictor.information) information_content() (chamois.predictor.ChemicalOntologyPredictor method) information_theoric_curve() (in module chamois.predictor.information) K kind (chamois.model.Domain attribute) (chamois.model.PfamDomain attribute) L load() (chamois.predictor.ChemicalOntologyPredictor class method) M misinformation_score() (in module chamois.predictor.information) module chamois.classyfire chamois.compositions chamois.domains chamois.model chamois.ontology chamois.orf chamois.predictor chamois.predictor.information N name (chamois.model.Domain attribute) (chamois.model.PfamDomain attribute) neighbors() (chamois.ontology.AdjacencyMatrix method) NoGeneFoundWarning (class in chamois.orf) O Ontology (class in chamois.ontology) ORFFinder (class in chamois.orf) overlaps() (chamois.model.PfamDomain method) P parents() (chamois.ontology.AdjacencyMatrix method) PfamAnnotator (class in chamois.domains) PfamDomain (class in chamois.model) predict() (chamois.predictor.ChemicalOntologyPredictor method) predict_probas() (chamois.predictor.ChemicalOntologyPredictor method) propagate() (chamois.predictor.ChemicalOntologyPredictor method) protein (chamois.model.Domain attribute) (chamois.model.PfamDomain attribute) Protein (class in chamois.model) pvalue (chamois.model.PfamDomain attribute) PyrodigalFinder (class in chamois.orf) Q Query (class in chamois.classyfire) query() (chamois.classyfire.Client method) R record (chamois.model.ClusterSequence attribute) remaining_uncertainty_score() (in module chamois.predictor.information) retrieve() (chamois.classyfire.Client method) S save() (chamois.predictor.ChemicalOntologyPredictor method) score (chamois.model.PfamDomain attribute) semantic_distance_score() (in module chamois.predictor.information) semantic_similarity (chamois.ontology.Ontology attribute) sequence (chamois.model.Protein attribute) similarity() (chamois.ontology.Ontology method) source (chamois.model.ClusterSequence attribute) start (chamois.model.PfamDomain attribute) status (chamois.classyfire.Query property) T Term (class in chamois.classyfire) terms (chamois.classyfire.Classification property) total (chamois.domains.DomainAnnotator property) (chamois.domains.PfamAnnotator property) trained() (chamois.predictor.ChemicalOntologyPredictor class method) U url (chamois.classyfire.Term property) W weighted_information_theoric_curve() (in module chamois.predictor.information) weighted_precision_recall_curve() (in module chamois.predictor.information)
