Index

_

_classes (orthrus.core.pipeline.Score attribute) _classes_handle (orthrus.core.pipeline.Classify attribute) _f_ranks_handle (orthrus.core.pipeline.FeatureSelect attribute) _f_weights_handle (orthrus.core.pipeline.Classify attribute) _fit_handle (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Transform attribute)

_fit_transform_handle (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Transform attribute) _infer_class_labels_on_output (orthrus.core.pipeline.Score attribute) _predict_handle (orthrus.core.pipeline.Classify attribute) _s_weights_handle (orthrus.core.pipeline.Classify attribute) _sample_weight_attr (orthrus.core.pipeline.Score attribute) _transform_handle (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Transform attribute)

A

align_embedding() (in module orthrus.decomposition.general)

autosummarize() (orthrus.core.dataset.DataSet method)

B

batch_jobs_() (in module orthrus.core.helper)

bias_ (orthrus.sparse.classifiers.svm.SSVMClassifier attribute)

C

checkpoint_path (orthrus.core.pipeline.Pipeline attribute) checkpoint_path() (orthrus.core.pipeline.Pipeline property) class_attr (orthrus.core.pipeline.Classify attribute) classes_ (orthrus.sparse.classifiers.svm.SSVMClassifier attribute) classifiers_ (orthrus.sparse.feature_selection.kffs.KFFS attribute) Classify (class in orthrus.core.pipeline) classify() (orthrus.core.dataset.DataSet method)

collapse_results() (orthrus.core.pipeline.Process method) compose() (in module orthrus.core.pipeline) condense_scores() (orthrus.core.pipeline.Score method) convert_type() (orthrus.solvers.linear.LPNewton method) (orthrus.sparse.classifiers.svm.L1SVM method) (orthrus.sparse.feature_selection.pathway_selection.PathwayScore method) coordinates (orthrus.decomposition.general.OrthTransform attribute)

D

data (orthrus.core.dataset.DataSet attribute) DataSet (class in orthrus.core.dataset) decision_function() (orthrus.sparse.classifiers.svm.SSVMClassifier method)

default_val() (in module orthrus.core.helper) description (orthrus.core.dataset.DataSet attribute) diagnostic_information_ (orthrus.sparse.feature_selection.IterativeFeatureRemoval.IFR attribute) dissimilarity_matrix (orthrus.core.dataset.DataSet attribute)

E

eigenvalues_ (orthrus.manifold.mds.MDS attribute) eigenvectors_ (orthrus.manifold.mds.MDS attribute)

embedding_ (orthrus.manifold.mds.MDS attribute) experiments (orthrus.core.dataset.DataSet attribute) extract_result() (orthrus.core.pipeline.Process method)

F

feature_select() (orthrus.core.dataset.DataSet method) FeatureSelect (class in orthrus.core.pipeline) Fit (class in orthrus.core.pipeline) fit() (orthrus.decomposition.general.OrthTransform method) (orthrus.manifold.mds.MDS method) (orthrus.preprocessing.normalizations.LogNormalizer method) (orthrus.sparse.classifiers.svm.L1SVM method) (orthrus.sparse.classifiers.svm.SSVMClassifier method) (orthrus.sparse.classifiers.svm.SSVMSelect method) (orthrus.sparse.feature_selection.IterativeFeatureRemoval.IFR method) (orthrus.sparse.feature_selection.kffs.KFFS method) (orthrus.sparse.feature_selection.kfold_loso_ifr.KFLIFR method) (orthrus.sparse.feature_selection.kfold_shuffle_ifr.KFSIFR method) (orthrus.sparse.feature_selection.pathway_selection.PathwayScore method) (orthrus.sparse.feature_selection.pca_snr_selection.PCASNR method) (orthrus.sparse.feature_selection.sabs.SABS method)

fit_args (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Transform attribute) fit_transform() (orthrus.decomposition.general.OrthTransform method) (orthrus.manifold.mds.MDS method) (orthrus.preprocessing.batch_corrections.Harmony method) (orthrus.preprocessing.batch_corrections.Limma method) (orthrus.preprocessing.normalizations.LogNormalizer method) (orthrus.preprocessing.normalizations.MedianFoldChangeNormalizer method) from_ccd() (in module orthrus.core.dataset)

G

generate_attr_from_queries() (orthrus.core.dataset.DataSet method) generate_experiment() (in module orthrus.core.helper) generate_project() (in module orthrus.core.helper) generate_save_path() (in module orthrus.core.helper)

get_batch_correction_matric_for_ranked_features() (in module orthrus.sparse.feature_selection.helper) get_close_matches_icase() (in module orthrus.core.helper) get_correlates() (in module orthrus.sparse.feature_selection.helper) get_top_95_features() (in module orthrus.sparse.feature_selection.helper)

H

Harmony (class in orthrus.preprocessing.batch_corrections)

I

IFR (class in orthrus.sparse.feature_selection.IterativeFeatureRemoval)

imputation_method (orthrus.core.dataset.DataSet attribute) impute() (orthrus.core.dataset.DataSet method)

K

KFFS (class in orthrus.sparse.feature_selection.kffs)

KFLIFR (class in orthrus.sparse.feature_selection.kfold_loso_ifr) KFSIFR (class in orthrus.sparse.feature_selection.kfold_shuffle_ifr)

L

L1SVM (class in orthrus.sparse.classifiers.svm) Limma (class in orthrus.preprocessing.batch_corrections) load_dataset() (in module orthrus.core.dataset)

load_object() (in module orthrus.core.helper) LogNormalizer (class in orthrus.preprocessing.normalizations) LPNewton (class in orthrus.solvers.linear) LPPrimalDualPy() (in module orthrus.solvers.linear)

M

MDS (class in orthrus.manifold.mds) MedianFoldChangeNormalizer (class in orthrus.preprocessing.normalizations) metadata (orthrus.core.dataset.DataSet attribute) method_exists() (in module orthrus.core.helper) module orthrus.core.dataset orthrus.core.helper orthrus.core.pipeline orthrus.core.scratch orthrus.decomposition.general orthrus.manifold.mds orthrus.model_selection.partitioning orthrus.preprocessing.batch_corrections orthrus.preprocessing.normalizations orthrus.solvers.linear orthrus.sparse.classifiers.svm orthrus.sparse.feature_selection.helper orthrus.sparse.feature_selection.IterativeFeatureRemoval orthrus.sparse.feature_selection.kffs orthrus.sparse.feature_selection.kfold_loso_ifr orthrus.sparse.feature_selection.kfold_shuffle_ifr orthrus.sparse.feature_selection.pathway_selection orthrus.sparse.feature_selection.pca_snr_selection orthrus.sparse.feature_selection.sabs

module_from_path() (in module orthrus.core.helper)

N

n_features (orthrus.core.dataset.DataSet attribute) n_features() (orthrus.core.dataset.DataSet property) n_samples (orthrus.core.dataset.DataSet attribute) n_samples() (orthrus.core.dataset.DataSet property)

name (orthrus.core.dataset.DataSet attribute) new_f_ids (orthrus.core.pipeline.Transform attribute) normalization_method (orthrus.core.dataset.DataSet attribute) normalize() (orthrus.core.dataset.DataSet method)

O

orthrus.core.dataset module orthrus.core.helper module orthrus.core.pipeline module orthrus.core.scratch module orthrus.decomposition.general module orthrus.manifold.mds module orthrus.model_selection.partitioning module orthrus.preprocessing.batch_corrections module orthrus.preprocessing.normalizations module orthrus.solvers.linear module

orthrus.sparse.classifiers.svm module orthrus.sparse.feature_selection.helper module orthrus.sparse.feature_selection.IterativeFeatureRemoval module orthrus.sparse.feature_selection.kffs module orthrus.sparse.feature_selection.kfold_loso_ifr module orthrus.sparse.feature_selection.kfold_shuffle_ifr module orthrus.sparse.feature_selection.pathway_selection module orthrus.sparse.feature_selection.pca_snr_selection module orthrus.sparse.feature_selection.sabs module OrthTransform (class in orthrus.decomposition.general)

P

parallel (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Partition attribute) (orthrus.core.pipeline.Pipeline attribute) (orthrus.core.pipeline.Process attribute) (orthrus.core.pipeline.Report attribute) (orthrus.core.pipeline.Score attribute) (orthrus.core.pipeline.Transform attribute) Partition (class in orthrus.core.pipeline) path (orthrus.core.dataset.DataSet attribute) PathwayScore (class in orthrus.sparse.feature_selection.pathway_selection) PCASNR (class in orthrus.sparse.feature_selection.pca_snr_selection) Pipeline (class in orthrus.core.pipeline) pipeline_name (orthrus.core.pipeline.Pipeline attribute) plot_basic_diagnostic_stats() (orthrus.sparse.feature_selection.IterativeFeatureRemoval.IFR method) plot_feature_frequency() (in module orthrus.sparse.feature_selection.helper) plot_scores() (in module orthrus.core.helper) plot_snrs() (orthrus.sparse.feature_selection.pca_snr_selection.PCASNR method) plot_weights() (orthrus.sparse.classifiers.svm.SSVMSelect method) pop_first_element() (in module orthrus.core.helper) pred_labels_ (orthrus.sparse.classifiers.svm.SSVMClassifier attribute)

pred_type (orthrus.core.pipeline.Score attribute) predict() (orthrus.sparse.classifiers.svm.L1SVM method) (orthrus.sparse.classifiers.svm.SSVMClassifier method) predict_args (orthrus.core.pipeline.Classify attribute) prefit (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Transform attribute) print_description() (orthrus.core.dataset.DataSet method) Process (class in orthrus.core.pipeline) process (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Partition attribute) (orthrus.core.pipeline.Process attribute) (orthrus.core.pipeline.Score attribute) (orthrus.core.pipeline.Transform attribute) process_name (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Score attribute) (orthrus.core.pipeline.Transform attribute) process_name() (orthrus.core.pipeline.Pipeline property) (orthrus.core.pipeline.Process property) processes (orthrus.core.pipeline.Pipeline attribute)

R

rank_features_by_attribute() (in module orthrus.sparse.feature_selection.helper) rank_features_by_mean_attribute_value() (in module orthrus.sparse.feature_selection.helper) rank_features_within_attribute_class() (in module orthrus.sparse.feature_selection.helper) ranks_ (orthrus.sparse.feature_selection.kffs.KFFS attribute) reduce_feature_set_size() (in module orthrus.sparse.feature_selection.helper) ReduceIFRFeatures (class in orthrus.sparse.feature_selection.helper) reformat_metadata() (orthrus.core.dataset.DataSet method) Report (class in orthrus.core.pipeline) report() (orthrus.core.pipeline.Report method) results_ (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Partition attribute) (orthrus.core.pipeline.Pipeline attribute) (orthrus.core.pipeline.Process attribute) (orthrus.core.pipeline.Score attribute) (orthrus.core.pipeline.Transform attribute) (orthrus.sparse.feature_selection.kffs.KFFS attribute) (orthrus.sparse.feature_selection.kfold_loso_ifr.KFLIFR attribute) (orthrus.sparse.feature_selection.kfold_shuffle_ifr.KFSIFR attribute)

retain_f_ids (orthrus.core.pipeline.Transform attribute) run() (orthrus.core.pipeline.Partition method) (orthrus.core.pipeline.Pipeline method) (orthrus.core.pipeline.Process method) (orthrus.core.pipeline.Score method) run_status_ (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Partition attribute) (orthrus.core.pipeline.Pipeline attribute) (orthrus.core.pipeline.Process attribute) (orthrus.core.pipeline.Score attribute) (orthrus.core.pipeline.Transform attribute)

S

SABS (class in orthrus.sparse.feature_selection.sabs) save() (orthrus.core.dataset.DataSet method) (orthrus.core.pipeline.Process method) save_object() (in module orthrus.core.helper) save_results() (orthrus.core.pipeline.Process method) scatter_plotly() (in module orthrus.core.helper) scatter_pyplot() (in module orthrus.core.helper) Score (class in orthrus.core.pipeline) score_args (orthrus.core.pipeline.Score attribute) select_features() (orthrus.sparse.classifiers.svm.SSVMSelect method) select_features_for_data_partition (orthrus.sparse.feature_selection.IterativeFeatureRemoval.IFR attribute) slice_dataset() (orthrus.core.dataset.DataSet method) sliding_window_classification_on_ranked_features() (in module orthrus.sparse.feature_selection.helper) snr() (orthrus.sparse.feature_selection.pca_snr_selection.PCASNR method)

solve() (orthrus.solvers.linear.LPNewton method) solver() (orthrus.sparse.classifiers.svm.SSVMClassifier property) split() (orthrus.model_selection.partitioning.TrainPartitioner method) (orthrus.model_selection.partitioning.TrainTestPartitioner method) split_args (orthrus.core.pipeline.Partition attribute) split_group (orthrus.core.pipeline.Partition attribute) split_handle (orthrus.core.pipeline.Partition attribute) SSVMClassifier (class in orthrus.sparse.classifiers.svm) SSVMSelect (class in orthrus.sparse.classifiers.svm) step() (orthrus.solvers.linear.LPNewton method) stop_before() (orthrus.core.pipeline.Pipeline property) supervised_attr (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Transform attribute)

T

TrainPartitioner (class in orthrus.model_selection.partitioning) TrainTestPartitioner (class in orthrus.model_selection.partitioning) Transform (class in orthrus.core.pipeline) transform() (orthrus.core.pipeline.FeatureSelect method) (orthrus.core.pipeline.Transform method) (orthrus.preprocessing.normalizations.LogNormalizer method) (orthrus.sparse.classifiers.svm.SSVMSelect method) (orthrus.sparse.feature_selection.IterativeFeatureRemoval.IFR method) (orthrus.sparse.feature_selection.kffs.KFFS method) (orthrus.sparse.feature_selection.kfold_shuffle_ifr.KFSIFR method) (orthrus.sparse.feature_selection.pathway_selection.PathwayScore method)

transform_args (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Transform attribute)

V

vardata (orthrus.core.dataset.DataSet attribute) (orthrus.core.pipeline.Transform attribute) venn_diagram() (orthrus.core.dataset.DataSet method) verbosity (orthrus.core.pipeline.Classify attribute) (orthrus.core.pipeline.FeatureSelect attribute) (orthrus.core.pipeline.Fit attribute) (orthrus.core.pipeline.Partition attribute) (orthrus.core.pipeline.Pipeline attribute) (orthrus.core.pipeline.Process attribute) (orthrus.core.pipeline.Score attribute) (orthrus.core.pipeline.Transform attribute)

visualize() (orthrus.core.dataset.DataSet method)

W

weights_ (orthrus.sparse.classifiers.svm.SSVMClassifier attribute)