Index

A

add_feature() (lncrnapy.data.Data method) Algorithm (class in lncrnapy.algorithms.algorithm)

all_features() (lncrnapy.data.Data method) attention() (in module lncrnapy.modules.bert)

B

BERT (class in lncrnapy.modules.bert) BLASTNIdXCov (class in lncrnapy.features.blast) BLASTNSearch (class in lncrnapy.features.blast) BLASTXBinary (class in lncrnapy.features.blast)

BLASTXSearch (class in lncrnapy.features.blast) BPELength (class in lncrnapy.features.tokenizers) BPEPieces (class in lncrnapy.features.tokenizers) BytePairEncoding (class in lncrnapy.features.tokenizers)

C

calculate() (lncrnapy.features.blast.BLASTNIdXCov method) (lncrnapy.features.blast.BLASTNSearch method) (lncrnapy.features.blast.BLASTXBinary method) (lncrnapy.features.blast.BLASTXSearch method) (lncrnapy.features.eiip.EIIPPhysicoChemical method) (lncrnapy.features.fickett.FickettScore method) (lncrnapy.features.general.Complexity method) (lncrnapy.features.general.Entropy method) (lncrnapy.features.general.EntropyDensityProfile method) (lncrnapy.features.general.GCContent method) (lncrnapy.features.general.Quality method) (lncrnapy.features.general.SequenceDistribution method) (lncrnapy.features.general.StdStopCodons method) (lncrnapy.features.kmer.KmerDistance method) (lncrnapy.features.kmer.KmerFreqs method) (lncrnapy.features.kmer.KmerScore method) (lncrnapy.features.mlcds.MLCDS method) (lncrnapy.features.mlcds.MLCDSLength method) (lncrnapy.features.mlcds.MLCDSLengthPercentage method) (lncrnapy.features.mlcds.MLCDSLengthStd method) (lncrnapy.features.mlcds.MLCDSScoreDistance method) (lncrnapy.features.mlcds.MLCDSScoreStd method) (lncrnapy.features.mlm_accuracy.MLMAccuracy method) (lncrnapy.features.orf.ORFAminoAcidFreqs method) (lncrnapy.features.orf.ORFCoordinates method) (lncrnapy.features.orf.ORFCoverage method) (lncrnapy.features.orf.ORFLength method) (lncrnapy.features.orf.ORFProtein method) (lncrnapy.features.orf.ORFProteinAnalysis method) (lncrnapy.features.orf.UTRCoverage method) (lncrnapy.features.orf.UTRLength method) (lncrnapy.features.sse.SSE method) (lncrnapy.features.sse.UPFrequency method) (lncrnapy.features.standardizer.Standardizer method) (lncrnapy.features.tokenizers.BPELength method) (lncrnapy.features.tokenizers.BPEPieces method) (lncrnapy.features.tokenizers.BytePairEncoding method) (lncrnapy.features.tokenizers.KmerTokenizer method) (lncrnapy.features.tokenizers.TokenLocalization method) (lncrnapy.features.zhang.ZhangScore method) (lncrnapy.selection.methods.MDSSelection method)

calculate_ant_matrix() (lncrnapy.features.mlcds.MLCDS method) calculate_edp() (lncrnapy.features.general.EntropyDensityProfile method) calculate_feature() (lncrnapy.data.Data method) calculate_kmer_freqs() (lncrnapy.features.kmer.KmerBase method) calculate_kmer_tokens() (lncrnapy.features.tokenizers.KmerTokenizer method) calculate_per_sequence() (lncrnapy.features.blast.BLASTXSearch method) (lncrnapy.features.eiip.EIIPPhysicoChemical method) (lncrnapy.features.fickett.FickettScore method) (lncrnapy.features.general.Complexity method) (lncrnapy.features.general.GCContent method) (lncrnapy.features.general.SequenceDistribution method) (lncrnapy.features.general.StdStopCodons method) (lncrnapy.features.kmer.KmerScore method) (lncrnapy.features.mlcds.MLCDS method) (lncrnapy.features.orf.ORFAminoAcidFreqs method) (lncrnapy.features.orf.ORFCoordinates method) (lncrnapy.features.orf.ORFProtein method) (lncrnapy.features.orf.ORFProteinAnalysis method) (lncrnapy.features.sse.SSE method) (lncrnapy.features.sse.UPFrequency method) (lncrnapy.features.zhang.ZhangScore method) calculate_power_spectrum() (lncrnapy.features.eiip.EIIPPhysicoChemical method) change_device() (in module lncrnapy.utils) check_columns() (lncrnapy.data.Data method) (lncrnapy.features.sequence_base.SequenceBase method) classification_metrics (in module lncrnapy.train.metrics) Classifier (class in lncrnapy.modules.wrappers) CLIP_NORM (in module lncrnapy.utils) CNCI (class in lncrnapy.algorithms.traditional) CNIT (class in lncrnapy.algorithms.traditional) coding_noncoding_split() (lncrnapy.data.Data method) Complexity (class in lncrnapy.features.general) ConvSeqEmbedding (class in lncrnapy.modules.conv_seq_encoding) ConvSeqEncoding (class in lncrnapy.modules.conv_seq_encoding) count_kmers() (lncrnapy.features.kmer.KmerScore method) coverage_table() (in module lncrnapy.features.tokenizers) CPAT (class in lncrnapy.algorithms.traditional) CPC (class in lncrnapy.algorithms.traditional) CPC2 (class in lncrnapy.algorithms.traditional) CPPred (class in lncrnapy.algorithms.traditional) CSEBERT (class in lncrnapy.modules.bert) CSEResNet (class in lncrnapy.modules.cnn)

D

Data (class in lncrnapy.data) Decoder (class in lncrnapy.modules.bert)

DeepCPP (class in lncrnapy.algorithms.traditional) DEVICE (in module lncrnapy.utils) DummyScaler (class in lncrnapy.train.mixed_precision)

E

EarlyStopping (class in lncrnapy.train.loggers) EIIPPhysicoChemical (class in lncrnapy.features.eiip) Encoder (class in lncrnapy.modules.bert) Entropy (class in lncrnapy.features.general) EntropyDensityProfile (class in lncrnapy.features.general) epoch() (in module lncrnapy.train.masked_conv_modeling) (in module lncrnapy.train.masked_token_modeling)

epoch_classifier() (in module lncrnapy.train.classification) epoch_regressor() (in module lncrnapy.train.regression) evaluate() (in module lncrnapy.train.masked_conv_modeling) (in module lncrnapy.train.masked_token_modeling) evaluate_classifier() (in module lncrnapy.train.classification) evaluate_regressor() (in module lncrnapy.train.regression)

F

feature_correlation() (lncrnapy.data.Data method) feature_extraction() (lncrnapy.algorithms.algorithm.Algorithm method) (lncrnapy.algorithms.traditional.PLEK method) feature_importance_analysis() (in module lncrnapy.selection.importance_analysis) FeatureSelectionBase (class in lncrnapy.selection.methods) FeedForward (class in lncrnapy.modules.bert) FEELnc (class in lncrnapy.algorithms.traditional) FickettScore (class in lncrnapy.features.fickett) filter_outliers() (lncrnapy.data.Data method) filter_sequence_quality() (lncrnapy.data.Data method) finish() (lncrnapy.train.loggers.LoggerBase method) fit() (lncrnapy.algorithms.algorithm.Algorithm method) ForestSelection (class in lncrnapy.selection.methods) forward() (lncrnapy.modules.bert.BERT method) (lncrnapy.modules.bert.CSEBERT method) (lncrnapy.modules.bert.Decoder method) (lncrnapy.modules.bert.Encoder method) (lncrnapy.modules.bert.FeedForward method) (lncrnapy.modules.bert.MultiHeadAttention method) (lncrnapy.modules.bert.PositionalEncoding method) (lncrnapy.modules.bert.ResidualConnection method) (lncrnapy.modules.cnn.CSEResNet method) (lncrnapy.modules.cnn.MycoAICNN method) (lncrnapy.modules.cnn.ResidualBlock method) (lncrnapy.modules.cnn.ResNet method) (lncrnapy.modules.conv_seq_encoding.ConvSeqEmbedding method) (lncrnapy.modules.conv_seq_encoding.ConvSeqEncoding method) (lncrnapy.modules.wrappers.Classifier method) (lncrnapy.modules.wrappers.MaskedConvModel method) (lncrnapy.modules.wrappers.MaskedTokenModel method) (lncrnapy.modules.wrappers.Regressor method) (lncrnapy.modules.wrappers.WrapperBase method)

frame_agreement() (in module lncrnapy.train.metrics) frame_consistency() (in module lncrnapy.train.metrics) freeze() (in module lncrnapy.utils) (lncrnapy.modules.bert.BERT method) (lncrnapy.modules.bert.CSEBERT method) freeze_kernels() (lncrnapy.modules.bert.CSEBERT method)

G

GCContent (class in lncrnapy.features.general) get_abs_coordinates() (lncrnapy.features.mlcds.MLCDS method) get_amp_args() (in module lncrnapy.train.mixed_precision) get_consecutive_indices() (in module lncrnapy.train.masked_conv_modeling) get_gencode_gene_names() (in module lncrnapy.data) get_gradient_scaler() (in module lncrnapy.train.mixed_precision)

get_hl_sse_sequence() (in module lncrnapy.features.sse) get_mlcds() (lncrnapy.features.mlcds.MLCDS method) get_piece_length_stats() (lncrnapy.features.tokenizers.BytePairEncoding method) get_random_nucs() (in module lncrnapy.train.masked_conv_modeling) get_reading_frame() (lncrnapy.features.mlcds.MLCDS method) get_rna_type_refseq() (in module lncrnapy.data)

I

imshow_ant_matrix() (lncrnapy.features.mlcds.MLCDS method) index_to_bool() (in module lncrnapy.train.masked_conv_modeling)

inverse_transform() (lncrnapy.features.standardizer.Standardizer method) iSeeRNA (class in lncrnapy.algorithms.traditional)

K

KmerBase (class in lncrnapy.features.kmer) KmerDistance (class in lncrnapy.features.kmer)

KmerFreqs (class in lncrnapy.features.kmer) KmerScore (class in lncrnapy.features.kmer) KmerTokenizer (class in lncrnapy.features.tokenizers)

L

latent_space() (lncrnapy.modules.wrappers.WrapperBase method) Length (class in lncrnapy.features.general) LncADeep (class in lncrnapy.algorithms.traditional) LncFinder (class in lncrnapy.algorithms.traditional) lncRNA_classification_report() (in module lncrnapy.evaluate) lncrnapy.algorithms module lncrnapy.algorithms.algorithm module lncrnapy.algorithms.traditional module lncrnapy.data module lncrnapy.evaluate module lncrnapy.features module lncrnapy.features.blast module lncrnapy.features.eiip module lncrnapy.features.fickett module lncrnapy.features.general module lncrnapy.features.kmer module lncrnapy.features.mlcds module lncrnapy.features.mlm_accuracy module lncrnapy.features.orf module lncrnapy.features.sequence_base module lncrnapy.features.sse module lncrnapy.features.standardizer module lncrnapy.features.tokenizers module lncrnapy.features.zhang module lncrnapy.modules module

lncrnapy.modules.bert module lncrnapy.modules.cnn module lncrnapy.modules.conv_seq_encoding module lncrnapy.modules.wrappers module lncrnapy.selection module lncrnapy.selection.importance_analysis module lncrnapy.selection.methods module lncrnapy.train module lncrnapy.train.classification module lncrnapy.train.loggers module lncrnapy.train.lr_schedule module lncrnapy.train.masked_conv_modeling module lncrnapy.train.masked_token_modeling module lncrnapy.train.metrics module lncrnapy.train.mixed_precision module lncrnapy.train.regression module lncrnapy.utils module loadtxt() (lncrnapy.features.fickett.FickettScore method) log() (lncrnapy.train.loggers.LoggerBase method) (lncrnapy.train.loggers.LoggerList method) LoggerBase (class in lncrnapy.train.loggers) LoggerDistribution (class in lncrnapy.train.loggers) LoggerList (class in lncrnapy.train.loggers) LoggerPlot (class in lncrnapy.train.loggers) LoggerPrint (class in lncrnapy.train.loggers) LoggerTokenCounts (class in lncrnapy.train.loggers) LoggerWrite (class in lncrnapy.train.loggers) LrSchedule (class in lncrnapy.train.lr_schedule)

M

mask_batch() (in module lncrnapy.train.masked_conv_modeling) (in module lncrnapy.train.masked_token_modeling) MaskedConvModel (class in lncrnapy.modules.wrappers) MaskedTokenModel (class in lncrnapy.modules.wrappers) mcm_metrics (in module lncrnapy.train.metrics) MDSSelection (class in lncrnapy.selection.methods) merge_fasta() (in module lncrnapy.data) MLCDS (class in lncrnapy.features.mlcds) MLCDSLength (class in lncrnapy.features.mlcds) MLCDSLengthPercentage (class in lncrnapy.features.mlcds) MLCDSLengthStd (class in lncrnapy.features.mlcds) MLCDSScoreDistance (class in lncrnapy.features.mlcds) MLCDSScoreStd (class in lncrnapy.features.mlcds) MLMAccuracy (class in lncrnapy.features.mlm_accuracy) module lncrnapy.algorithms lncrnapy.algorithms.algorithm lncrnapy.algorithms.traditional lncrnapy.data lncrnapy.evaluate lncrnapy.features lncrnapy.features.blast lncrnapy.features.eiip lncrnapy.features.fickett lncrnapy.features.general lncrnapy.features.kmer lncrnapy.features.mlcds lncrnapy.features.mlm_accuracy lncrnapy.features.orf lncrnapy.features.sequence_base lncrnapy.features.sse lncrnapy.features.standardizer lncrnapy.features.tokenizers lncrnapy.features.zhang lncrnapy.modules lncrnapy.modules.bert lncrnapy.modules.cnn lncrnapy.modules.conv_seq_encoding lncrnapy.modules.wrappers lncrnapy.selection lncrnapy.selection.importance_analysis lncrnapy.selection.methods lncrnapy.train lncrnapy.train.classification lncrnapy.train.loggers lncrnapy.train.lr_schedule lncrnapy.train.masked_conv_modeling lncrnapy.train.masked_token_modeling lncrnapy.train.metrics lncrnapy.train.mixed_precision lncrnapy.train.regression lncrnapy.utils

mtm_metrics (in module lncrnapy.train.metrics) MultiHeadAttention (class in lncrnapy.modules.bert) MycoAICNN (class in lncrnapy.modules.cnn)

N

no_orf_to_nan() (lncrnapy.features.orf.UTRLength method) NoSelection (class in lncrnapy.selection.methods)

NUC_TO_4D (in module lncrnapy.utils) nucleotide_frequencies() (lncrnapy.features.fickett.FickettScore method) num_coding_noncoding() (lncrnapy.data.Data method)

O

orf_column_names() (in module lncrnapy.features.orf) orf_prediction_metrics (in module lncrnapy.train.metrics) ORFAminoAcidFreqs (class in lncrnapy.features.orf) ORFCoordinates (class in lncrnapy.features.orf)

ORFCoverage (class in lncrnapy.features.orf) ORFIsoelectric (class in lncrnapy.features.orf) ORFLength (class in lncrnapy.features.orf) ORFProtein (class in lncrnapy.features.orf) ORFProteinAnalysis (class in lncrnapy.features.orf)

P

PermutationSelection (class in lncrnapy.selection.methods) PLEK (class in lncrnapy.algorithms.traditional) PLncPro (class in lncrnapy.algorithms.traditional) plot_bias() (lncrnapy.features.kmer.KmerScore method) plot_bpe_lengths() (in module lncrnapy.features.tokenizers) plot_cross_dataset_violins() (in module lncrnapy.data) plot_feature_boxplot() (lncrnapy.data.Data method) plot_feature_correlation() (lncrnapy.data.Data method) plot_feature_density() (lncrnapy.data.Data method) plot_feature_importance() (in module lncrnapy.selection.importance_analysis) plot_feature_scatter() (lncrnapy.data.Data method) plot_feature_selection_results() (in module lncrnapy.selection.importance_analysis)

plot_feature_space() (lncrnapy.data.Data method) plot_feature_violin() (lncrnapy.data.Data method) plot_history() (lncrnapy.train.loggers.LoggerPlot method) plot_refseq_labels() (in module lncrnapy.data) pos_weight() (lncrnapy.data.Data method) position_values() (lncrnapy.features.fickett.FickettScore method) PositionalEncoding (class in lncrnapy.modules.bert) predict() (lncrnapy.algorithms.algorithm.Algorithm method) (lncrnapy.modules.wrappers.Classifier method) (lncrnapy.modules.wrappers.WrapperBase method) print() (lncrnapy.features.tokenizers.BPEPieces method) progress (in module lncrnapy.utils)

Q

Quality (class in lncrnapy.features.general)

R

read_blastn_output() (lncrnapy.features.blast.BLASTNSearch method) read_blastx_output() (lncrnapy.features.blast.BLASTXSearch method) reduce_dimensionality() (in module lncrnapy.data) regression_distribution() (in module lncrnapy.train.metrics) regression_metrics (in module lncrnapy.train.metrics) RegressionSelection (class in lncrnapy.selection.methods) Regressor (class in lncrnapy.modules.wrappers)

replace_uncertain_bases() (lncrnapy.features.kmer.KmerBase method) ResidualBlock (class in lncrnapy.modules.cnn) ResidualConnection (class in lncrnapy.modules.bert) ResNet (class in lncrnapy.modules.cnn) RFESelection (class in lncrnapy.selection.methods) run_blastn() (lncrnapy.features.blast.BLASTNSearch method) run_blastx() (lncrnapy.features.blast.BLASTXSearch method)

S

sample() (lncrnapy.data.Data method) savetxt() (lncrnapy.features.fickett.FickettScore method) scale() (lncrnapy.train.mixed_precision.DummyScaler method) select_features() (lncrnapy.selection.methods.FeatureSelectionBase method) (lncrnapy.selection.methods.ForestSelection method) (lncrnapy.selection.methods.MDSSelection method) (lncrnapy.selection.methods.NoSelection method) (lncrnapy.selection.methods.PermutationSelection method) (lncrnapy.selection.methods.RegressionSelection method) (lncrnapy.selection.methods.RFESelection method) (lncrnapy.selection.methods.TTestSelection method) SequenceBase (class in lncrnapy.features.sequence_base)

SequenceDistribution (class in lncrnapy.features.general) set_random_reading_frame() (lncrnapy.data.Data method) set_tensor_features() (lncrnapy.data.Data method) sorted_feature_importance() (in module lncrnapy.selection.importance_analysis) split_refseq() (in module lncrnapy.data) SSE (class in lncrnapy.features.sse) Standardizer (class in lncrnapy.features.standardizer) start() (lncrnapy.train.loggers.LoggerBase method) (lncrnapy.train.loggers.LoggerList method) (lncrnapy.train.loggers.LoggerPlot method) StdStopCodons (class in lncrnapy.features.general) step() (lncrnapy.train.mixed_precision.DummyScaler method)

T

test_features() (lncrnapy.data.Data method) to_csv() (lncrnapy.data.Data method) to_fasta() (lncrnapy.data.Data method) to_hdf() (lncrnapy.data.Data method) TokenizerBase (class in lncrnapy.features.tokenizers) TokenLocalization (class in lncrnapy.features.tokenizers)

TOKENS (in module lncrnapy.utils) train_classifier() (in module lncrnapy.train.classification) train_masked_conv_modeling() (in module lncrnapy.train.masked_conv_modeling) train_masked_token_modeling() (in module lncrnapy.train.masked_token_modeling) train_regressor() (in module lncrnapy.train.regression) train_test_split() (lncrnapy.data.Data method) TTestSelection (class in lncrnapy.selection.methods)

U

unfreeze() (lncrnapy.modules.bert.BERT method) (lncrnapy.modules.bert.CSEBERT method) unscale_() (lncrnapy.train.mixed_precision.DummyScaler method)

update() (lncrnapy.train.mixed_precision.DummyScaler method) UPFrequency (class in lncrnapy.features.sse) UTRCoverage (class in lncrnapy.features.orf) UTRLength (class in lncrnapy.features.orf)

V

visualize() (lncrnapy.modules.conv_seq_encoding.ConvSeqEncoding method)

vocab_size (lncrnapy.features.tokenizers.BytePairEncoding property) (lncrnapy.features.tokenizers.TokenizerBase property)

W

watch_progress() (in module lncrnapy.utils)

WrapperBase (class in lncrnapy.modules.wrappers)

Z

ZhangScore (class in lncrnapy.features.zhang)